def test5(self):
regions = []
add = regions.append
add(makeReadRegion(0, '25M', 10, 34))
add(makeReadRegion(3, '1N', 35, 35))
add(makeReadRegion(1, '1M,1I', 35, 35))
add(makeReadRegion(0, '74M', 36, 109))
cb = cigarbuilder.CigarBuilder()
cigar = cb.build(regions)
self.assertEqual(cigarutils.simplify(cigar),[(0,26),(1,1),(0,74)])
def test2(self):
regions = []
add = regions.append
add(makeReadRegion(1, '1I', -1, -2))
add(makeReadRegion(2, '10I', 5, 4)) ## D_1 of I_0
add(makeReadRegion(1, '2I', 5, 4))
add(makeReadRegion(1, '3I', 5, 4))
add(makeReadRegion(2, '20I', 5, 4,)) ## D_1 of I_0
add(makeReadRegion(1, '4I', 5, 4 ))
add(makeReadRegion(1, '4I', 7, 6 ))
cb = cigarbuilder.CigarBuilder()
cigar = cb.build(regions)
self.assertEqual(cigar, [(1, 1), (1, 2), (1, 3), (1, 4), (1, 20), (2, 2), (1, 4)])
def test1(self):
regions = []
add = regions.append
## an inserted I_1 before any M_1
add(makeReadRegion(1, '2I', -1, -2))
add(makeReadRegion(0, '4M', 0, 3))
## an inserted I_1 after an M_1
add(makeReadRegion(1, '2I', -1, -1))
## an inserted I_1 after an inserted I_1
add(makeReadRegion(1, '3I', -1, -1))
## a gap
##
add(makeReadRegion(1, '1M', 5, 5))
## an inserted I_1 after a match I_1
add(makeReadRegion(1, '4I', 6, 5))
## a gap here
add(makeReadRegion(0, '2M', 7, 8))
## an M_1 that is an insertion
add(makeReadRegion(0, '2I', 9, 8))
add(makeReadRegion(1, '3I', 9, 8))
## an M_1 that is an insertion
add(makeReadRegion(0, '4I', 9, 8))
add(makeReadRegion(1, '5I', 9, 8))
## a gap here
add(makeReadRegion(0, '5M', 10, 14))
cb = cigarbuilder.CigarBuilder()
cigar = cb.build(regions)
print(cigar)
self.assertEqual(cigar, [(1, 2), (0, 4), (1, 2), (1, 3), (2, 1),
(1, 5), (2, 1), (0, 2), (1, 2), (1, 3),
(1, 4), (1, 5), (2, 1), (0, 5)])
self.assertEqual(cigarutils.toString(cigar),
'2I,4M,2I,3I,1D,1M,4I,1D,2M,2I,3I,4I,5I,1D,5M')
def test1(self):
regions = []
add = regions.append
add(makeReadRegion(1, '2I', -1, -2))## an inserted I_1 before any M_1
add(makeReadRegion(0, '4M', 0, 3))
add(makeReadRegion(1, '2I', -1, -1)) ## an inserted I_1 after an M_1
add(makeReadRegion(1, '3I', -1, -1)) ## an inserted I_1 after an inserted I_1
## a gap
add(makeReadRegion(1, '1M', 5, 5)) ## a match I_1 after is an inserted I_1
add(makeReadRegion(1, '4I', 6, 5)) ## an inserted I_1 after a match I_1
## a gap here
add(makeReadRegion(0, '2M', 7, 8))
add(makeReadRegion(0, '2I', 9, 8)) ## an M_1 that is an insertion
add(makeReadRegion(1, '3I', 9, 8))
add(makeReadRegion(0, '4I', 9, 8)) ## an M_1 that is an insertion
add(makeReadRegion(1, '5I', 9, 8))
## a gap here
add(makeReadRegion(0, '5M', 10, 14))
cb = cigarbuilder.CigarBuilder()
cigar = cb.build(regions)
print(cigar)
self.assertEqual(cigar, [(1, 2), (0, 4), (1, 2), (1, 3), (2, 1),
(0, 1), (1, 4), (2, 1), (0, 2), (1, 2),
(1, 3), (1, 4), (1, 5), (2, 1), (0, 5)])
self.assertEqual(cigarutils.toString(cigar), '2I,4M,2I,3I,1D,1M,4I,1D,2M,2I,3I,4I,5I,1D,5M')