def test_softclip_to_first_match_uncommonMatchOpOk(self):
util = cigar.CigarUtil(0, "1M")
self.assertEquals((45, "SS"
"XPNDISH"),
util._softclip_to_first_match(42, "SDNIP"
"XPNDISH"))
util = cigar.CigarUtil(0, "1M")
self.assertEquals((45, "SS"
"=PNDISH"),
util._softclip_to_first_match(42, "SDNIP"
"=PNDISH"))
def test_init_with_neitherCigarNorProfile(self):
util = cigar.CigarUtil(42, cigar="", cigar_profile="")
self.assertEquals("", util.cigar)
self.assertEquals("", util.cigar_profile)
self.assertEquals(42, util.reference_start)
util = cigar.CigarUtil(42, cigar=None, cigar_profile=None)
self.assertEquals("", util.cigar)
self.assertEquals("", util.cigar_profile)
self.assertEquals(42, util.reference_start)
util = cigar.CigarUtil(42)
self.assertEquals("", util.cigar)
self.assertEquals("", util.cigar_profile)
self.assertEquals(42, util.reference_start)
def test_assert_query_lengths_match(self):
base = cigar.CigarUtil(42, "10M")
trivially_matching = cigar.CigarUtil(42, "10M")
base._assert_query_lengths_match(trivially_matching)
subtly_matching = cigar.CigarUtil(42, "2M15N8S")
base._assert_query_lengths_match(subtly_matching)
not_matching = cigar.CigarUtil(42, "2S8M2S")
self.assertRaisesRegexp(
katana.util.KatanaException,
r"Old CIGAR query length.*10M.*10.*2S8M2S.*12.*",
base._assert_query_lengths_match, not_matching)
def test_partition_cigar_refNonconsumingOpsWithFlankingSoftclips(self):
util = cigar.CigarUtil(42, "5S" "5M" "4I" "1M" "5S")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(37, "5S"), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "4I1M5S"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(37, "5S5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48, "5S"), c3)
(c1, c2, c3) = util._partition_cigar(48, 53)
self.assertEquals(cigar.CigarUtil(37, "5S5M4I1M"), c1)
self.assertEquals(cigar.CigarUtil(48, "5S"), c2)
self.assertEquals(cigar.CigarUtil(53, ""), c3)
def test_softclip_replacesConsumingOpsWithSoftClips(self):
util = cigar.CigarUtil(0, "1M")
self.assertEquals("HS"
"SSSS"
"SH", util._softclip(cigar_profile="HS"
"MI=X"
"SH"))
def test_partition_cigar_targetRegionBoundedByShortReverseRead(self):
util = cigar.CigarUtil(100, "20M")
(c1, c2, c3) = util._partition_cigar(90, 120)
self.assertEquals(100, c1.reference_start)
self.assertEquals("", c1.cigar)
self.assertEquals(100, c2.reference_start)
self.assertEquals("20M", c2.cigar)
self.assertEquals(120, c3.reference_start)
self.assertEquals("", c3.cigar)
def test_softclip_target_flankingSoftclips(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
# 4444444444
# 0123456789
# SSMMMMMMSS
# SSSMMMMSSS
new_util = util.softclip_target(43, 47)
self.assertEquals("3S4M3S", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_flankingHardclips(self):
util = cigar.CigarUtil(42, "2H1S" "4M" "1S2H")
#3444444444
#9012345678
#HHSMMMMSHH
#HHSSMMSSHH
new_util = util.softclip_target(43, 45)
self.assertEquals("2H2S" "2M" "2S2H", new_util.cigar)
self.assertEquals(43, new_util.reference_start)
def test_softclip_target_deletes(self):
util = cigar.CigarUtil(42, "2M3D" "4M" "1S")
#4444444455
#2345678901
#MMDDD
# MMMM
# S
#SS MMMMS
new_util = util.softclip_target(47, 51)
self.assertEquals("2S" "4M" "1S", new_util.cigar)
self.assertEquals(47, new_util.reference_start)
def test_ref_consuming(self):
util = cigar.CigarUtil(0, "1M")
self.assertEquals(True, util._is_ref_consuming("M"))
self.assertEquals(False, util._is_ref_consuming("I"))
self.assertEquals(True, util._is_ref_consuming("S"))
self.assertEquals(True, util._is_ref_consuming("="))
self.assertEquals(True, util._is_ref_consuming("X"))
self.assertEquals(True, util._is_ref_consuming("D"))
self.assertEquals(True, util._is_ref_consuming("N"))
self.assertEquals(False, util._is_ref_consuming("H"))
self.assertEquals(False, util._is_ref_consuming("P"))
def test_partition_cigar_refNonconsumingOps(self):
util = cigar.CigarUtil(42, "5M4I1M")
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42, ""), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c3)
(c1, c2, c3) = util._partition_cigar(47, 48)
self.assertEquals(cigar.CigarUtil(42, "5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "4I1M"), c2)
self.assertEquals(cigar.CigarUtil(48, ""), c3)
def test_softclip_target_edgeInsert(self):
util = cigar.CigarUtil(42, "3M" "1I4M" "2X")
#444 444445
#234 567890
#ATAAACGTAC
#MMMI
# MMMM
# XX
#SSSSMMMMSS
new_util = util.softclip_target(45, 49)
self.assertEquals("4S" "4M" "2S", new_util.cigar)
self.assertEquals(45, new_util.reference_start)
def test_softclip_target_edgeDelete(self):
util = cigar.CigarUtil(42, "3M" "1D5M" "2S")
#44444444555
#23456789012
#ATA ACGTACG
#MMM
# DMMMM
# MSS
#SSS MMMMSSS
new_util = util.softclip_target(45, 50)
self.assertEquals("3S" "4M" "3S", new_util.cigar)
self.assertEquals(46, new_util.reference_start)
def test_partition_cigar_refConsumingOps(self):
util = cigar.CigarUtil(42, "5M5X")
# | 4444444455
# | 2345678901
# | MMMMM
# | XXXXX
(c1, c2, c3) = util._partition_cigar(42, 47)
self.assertEquals(cigar.CigarUtil(42, ""), c1)
self.assertEquals(cigar.CigarUtil(42, "5M"), c2)
self.assertEquals(cigar.CigarUtil(47, "5X"), c3)
(c1, c2, c3) = util._partition_cigar(47, 52)
self.assertEquals(cigar.CigarUtil(42, "5M"), c1)
self.assertEquals(cigar.CigarUtil(47, "5X"), c2)
self.assertEquals(cigar.CigarUtil(52, ""), c3)
def test_cigar_profile(self):
util = cigar.CigarUtil(42, "5M1I4S")
self.assertEquals("MMMMMISSSS", util.cigar_profile)
def test_repr(self):
base = cigar.CigarUtil(42, "10M")
match = re.match("<.*(cigar.*?)'>(.*)", repr(base))
eval_repr = match.group(1) + match.group(2)
#pylint: disable=eval-used
self.assertEquals(base, eval(eval_repr))
def test_eq(self):
base = cigar.CigarUtil(42, "10M")
self.assertEquals(base, cigar.CigarUtil(42, "10M"))
self.assertNotEquals(base, cigar.CigarUtil(10, "10M"))
self.assertNotEquals(base, cigar.CigarUtil(42, "1M"))
def test_pos_profiles_insertOk(self):
util = cigar.CigarUtil(0, "1M")
actual = util._pos_profiles("SIM")
self.assertEquals((1, ["S", "IM"]), actual)
def test_init_inconsistentCigarProfileDoesNotFail(self):
util = cigar.CigarUtil(42, cigar="10M", cigar_profile="XXMMM")
self.assertEquals("10M", util.cigar)
self.assertEquals("XXMMM", util.cigar_profile)
self.assertEquals(42, util.reference_start)
def test_init_withProfile(self):
util = cigar.CigarUtil(42, cigar_profile="XXMMM")
self.assertEquals("2X3M", util.cigar)
self.assertEquals("XXMMM", util.cigar_profile)
self.assertEquals(42, util.reference_start)
def test_softclip_target_validatesLength(self):
base = cigar.CigarUtil(42, "10M")
base.query_length = 100
self.assertRaises(katana.util.KatanaException, base.softclip_target,
44, 50)
def test_init_valid(self):
util = cigar.CigarUtil(42, "1M1I1D1N1=1X" "1H1S")
self.assertEquals(True, util.is_valid)
def test_init(self):
util = cigar.CigarUtil(42, "10M")
self.assertEquals("10M", util.cigar)
self.assertEquals(42, util.reference_start)
def test_pos_profiles_trailingHardclips(self):
util = cigar.CigarUtil(0, "1M")
actual = util._pos_profiles("SDMHH")
self.assertEquals((2, ["S", "D", "M", "HH"]), actual)
def test_pos_profiles_deleteOk(self):
util = cigar.CigarUtil(0, "1M")
actual = util._pos_profiles("SDM")
self.assertEquals((2, ["S", "D", "M"]), actual)
def test_partition_outOfBounds(self):
# ref | 4444444444
# | 0123456789
# read | SSMMMMMXX
# index | 210123456
util = cigar.CigarUtil(42, "2S" "6M" "2X")
(c1, c2, c3) = util._partition_cigar(30, 42)
self.assertEquals(cigar.CigarUtil(40, ""), c1)
self.assertEquals(cigar.CigarUtil(40, "2S"), c2)
self.assertEquals(cigar.CigarUtil(42, "6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(48, 60)
self.assertEquals(cigar.CigarUtil(40, "2S6M"), c1)
self.assertEquals(cigar.CigarUtil(48, "2X"), c2)
self.assertEquals(cigar.CigarUtil(50, ""), c3)
(c1, c2, c3) = util._partition_cigar(20, 30)
self.assertEquals(cigar.CigarUtil(40, ""), c1)
self.assertEquals(cigar.CigarUtil(40, ""), c2)
self.assertEquals(cigar.CigarUtil(40, "2S6M2X"), c3)
(c1, c2, c3) = util._partition_cigar(100, 110)
self.assertEquals(cigar.CigarUtil(40, "2S6M2X"), c1)
self.assertEquals(cigar.CigarUtil(50, ""), c2)
self.assertEquals(cigar.CigarUtil(50, ""), c3)
def test_cigar_profile_longer(self):
util = cigar.CigarUtil(42, "10M1I1D10H")
self.assertEquals("MMMMMMMMMMIDHHHHHHHHHH", util.cigar_profile)
def test_init_invalid(self):
util = cigar.CigarUtil(42, "1H1S")
self.assertEquals(False, util.is_valid)
def test_partition_cigar(self):
util = cigar.CigarUtil(42, "2S" "6M" "2S")
(c1, c2, c3) = util._partition_cigar(42, 48)
self.assertEquals(cigar.CigarUtil(40, "2S"), c1)
self.assertEquals(cigar.CigarUtil(42, "6M"), c2)
self.assertEquals(cigar.CigarUtil(48, "2S"), c3)
def test_softclip_target(self):
util = cigar.CigarUtil(42, "10M")
new_util = util.softclip_target(44, 50)
self.assertEquals("2S6M2S", new_util.cigar)
self.assertEquals(44, new_util.reference_start)
