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')