import unittest import os import pyfastaq from pymummer import alignment, snp, variant data_dir = "tests/data" class TestNucmer(unittest.TestCase): def test_init_nucmer(self): """test __init__ nucmer""" line = "\t".join( [ "1", "100", "2", "200", "101", "202", "42.42", "123", "456", "-1", "0", "ref", "qry", "[FOO]", ] ) a = alignment.Alignment(line) self.assertEqual(a.ref_start, 0) self.assertEqual(a.ref_end, 99) self.assertEqual(a.qry_start, 1) self.assertEqual(a.qry_end, 199) self.assertEqual(a.hit_length_ref, 101) self.assertEqual(a.hit_length_qry, 202) self.assertEqual(a.percent_identity, 42.42) self.assertEqual(a.ref_length, 123) self.assertEqual(a.qry_length, 456) self.assertEqual(a.frame, -1) self.assertEqual(a.ref_name, "ref") self.assertEqual(a.qry_name, "qry") def test_init_promer(self): """test __init__ promer""" line = "\t".join( [ "1", "1398", "4891054", "4892445", "1398", "1392", "89.55", "93.18", "0.21", "1398", "5349013", "1", "1", "ref", "qry", "[CONTAINED]", ] ) a = alignment.Alignment(line) self.assertEqual(a.ref_start, 0) self.assertEqual(a.ref_end, 1397) self.assertEqual(a.qry_start, 4891053) self.assertEqual(a.qry_end, 4892444) self.assertEqual(a.hit_length_ref, 1398) self.assertEqual(a.hit_length_qry, 1392) self.assertEqual(a.percent_identity, 89.55) self.assertEqual(a.ref_length, 1398) self.assertEqual(a.qry_length, 5349013) self.assertEqual(a.frame, 1) self.assertEqual(a.ref_name, "ref") self.assertEqual(a.qry_name, "qry") def test_swap(self): """test swap""" l_in = [ "1", "100", "2", "200", "101", "202", "42.42", "123", "456", "-1", "0", "ref", "qry", ] l_out = [ "2", "200", "1", "100", "202", "101", "42.42", "456", "123", "-1", "0", "qry", "ref", ] a_in = alignment.Alignment("\t".join(l_in)) a_in._swap() self.assertEqual(a_in, alignment.Alignment("\t".join(l_out))) a_in._swap() self.assertEqual(a_in, alignment.Alignment("\t".join(l_in))) def test_qry_coords(self): """Test qry_coords""" hits = [ "\t".join( [ "1", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "qry", ] ), "\t".join( [ "1", "101", "100", "1", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "qry", ] ), ] for h in hits: a = alignment.Alignment(h) self.assertEqual(pyfastaq.intervals.Interval(0, 99), a.qry_coords()) def test_ref_coords(self): """Test ref_coords""" hits = [ "\t".join( [ "1", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ), "\t".join( [ "100", "1", "100", "1", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ), ] for h in hits: a = alignment.Alignment(h) self.assertEqual(pyfastaq.intervals.Interval(0, 99), a.ref_coords()) def test_on_same_strand(self): """test on_same_strand""" self.assertTrue( alignment.Alignment( "\t".join( [ "1", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ) ).on_same_strand() ) self.assertTrue( alignment.Alignment( "\t".join( [ "100", "1", "100", "1", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ) ).on_same_strand() ) self.assertFalse( alignment.Alignment( "\t".join( [ "1", "100", "100", "1", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ) ).on_same_strand() ) self.assertFalse( alignment.Alignment( "\t".join( [ "100", "1", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ) ).on_same_strand() ) def test_is_self_hit(self): """Test is_self_hit""" tests = [ ( "\t".join( [ "1", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ), True, ), ( "\t".join( [ "1", "101", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ), False, ), ( "\t".join( [ "2", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref", ] ), False, ), ( "\t".join( [ "1", "100", "1", "100", "100", "100", "100.00", "1000", "1000", "1", "1", "ref", "ref2", ] ), False, ), ( "\t".join( [ "1", "100", "1", "100", "100", "100", "99.9", "1000", "1000", "1", "1", "ref", "ref", ] ), False, ), ] for t in tests: a = alignment.Alignment(t[0]) self.assertEqual(a.is_self_hit(), t[1]) def test_reverse_reference(self): """Test reverse_reference""" aln = alignment.Alignment( "\t".join( [ "100", "142", "1", "42", "43", "42", "100.00", "150", "100", "1", "1", "ref", "qry", ] ) ) expected = alignment.Alignment( "\t".join( [ "51", "9", "1", "42", "43", "42", "100.00", "150", "100", "1", "1", "ref", "qry", ] ) ) aln.reverse_reference() self.assertEqual(expected, aln) def test_reverse_query(self): """Test reverse_query""" aln = alignment.Alignment( "\t".join( [ "100", "142", "1", "42", "43", "42", "100.00", "150", "100", "1", "1", "ref", "qry", ] ) ) expected = alignment.Alignment( "\t".join( [ "100", "142", "100", "59", "43", "42", "100.00", "150", "100", "1", "1", "ref", "qry", ] ) ) aln.reverse_query() self.assertEqual(expected, aln) def test_str(self): """Test __str__""" l_in = [ "1", "100", "2", "200", "101", "202", "42.42", "123", "456", "-1", "0", "ref", "qry", ] # the 10th column (counting from zero) is ignored and so not output by __str__ l_out = l_in[:10] + l_in[11:] a = alignment.Alignment("\t".join(l_in)) self.assertEqual(str(a), "\t".join(l_out)) def test_to_msp_crunch(self): """Test to_msp_crunch""" l_in = [ "100", "110", "1", "10", "10", "11", "80.00", "123", "456", "-1", "0", "ref", "qry", ] a = alignment.Alignment("\t".join(l_in)) expected = "8 80.00 1 10 qry 100 110 ref" self.assertEqual(expected, a.to_msp_crunch()) def test_intersects_variant(self): "Test intersects_variant" "" snp0 = snp.Snp( "100\tA\t.\t600\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry" ) # 100 in ref, 600 in qry indel = variant.Variant(snp0) aln1 = alignment.Alignment( "100\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry" ) aln2 = alignment.Alignment( "101\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry" ) aln3 = alignment.Alignment( "100\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry" ) aln4 = alignment.Alignment( "101\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry" ) self.assertTrue(aln1.intersects_variant(indel)) self.assertFalse(aln2.intersects_variant(indel)) self.assertFalse(aln3.intersects_variant(indel)) self.assertFalse(aln4.intersects_variant(indel)) def test_qry_coords_from_ref_coord_test_bad_ref_coord(self): """Test qry_coords_from_ref_coord with bad ref coords""" aln = alignment.Alignment( "\t".join( [ "100", "200", "1", "100", "100", "100", "100.00", "300", "300", "1", "1", "ref", "qry", ] ) ) with self.assertRaises(alignment.Error): got = aln.qry_coords_from_ref_coord(98, []) with self.assertRaises(alignment.Error): got = aln.qry_coords_from_ref_coord(200, []) def test_qry_coords_from_ref_coord_test_same_strand(self): """Test qry_coords_from_ref_coord on same strand""" aln = alignment.Alignment( "\t".join( [ "100", "200", "1", "101", "100", "100", "100.00", "300", "300", "1", "1", "ref", "qry", ] ) ) snp0 = snp.Snp( "\t".join( ["140", "A", "T", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # snp snp0 = variant.Variant(snp0) snp1 = snp.Snp( "\t".join( ["140", "A", ".", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry snp2 = snp.Snp( "\t".join( ["141", "C", ".", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry del1 = variant.Variant(snp1) del2 = variant.Variant(snp1) self.assertTrue(del2.update_indel(snp2)) snp3 = snp.Snp( "\t".join( ["150", ".", "A", "50", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref snp4 = snp.Snp( "\t".join( ["150", ".", "C", "51", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref snp5 = snp.Snp( "\t".join( ["150", ".", "G", "52", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref ins1 = variant.Variant(snp3) ins2 = variant.Variant(snp3) self.assertTrue(ins2.update_indel(snp4)) self.assertTrue(ins2.update_indel(snp5)) tests = [ (99, [], (0, False)), (100, [], (1, False)), (199, [], (100, False)), (119, [del1], (20, False)), (149, [], (50, False)), (149, [del1], (49, False)), (149, [del2], (48, False)), (159, [], (60, False)), (159, [ins1], (61, False)), (159, [ins2], (63, False)), (159, [del1, ins1], (60, False)), (159, [del1, ins2], (62, False)), (159, [del2, ins1], (59, False)), (159, [del2, ins2], (61, False)), (139, [del1], (39, True)), (139, [snp0], (40, False)), (149, [ins1], (49, True)), ] for ref_coord, variant_list, expected in tests: got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) # if we reverse the direction of hit in query and reference, should get the same answer aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start def test_qry_coords_from_ref_coord_test_different_strand(self): """Test qry_coords_from_ref_coord on different strand""" aln = alignment.Alignment( "\t".join( [ "100", "200", "101", "1", "100", "100", "100.00", "300", "300", "1", "1", "ref", "qry", ] ) ) snp0 = snp.Snp( "\t".join( ["140", "A", "T", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # snp snp0 = variant.Variant(snp0) snp1 = snp.Snp( "\t".join( ["140", "A", ".", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry snp2 = snp.Snp( "\t".join( ["141", "C", ".", "40", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry del1 = variant.Variant(snp1) del2 = variant.Variant(snp1) self.assertTrue(del2.update_indel(snp2)) snp3 = snp.Snp( "\t".join( ["150", ".", "A", "50", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref snp4 = snp.Snp( "\t".join( ["150", ".", "C", "51", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref snp5 = snp.Snp( "\t".join( ["150", ".", "G", "52", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref ins1 = variant.Variant(snp3) ins2 = variant.Variant(snp3) self.assertTrue(ins2.update_indel(snp4)) self.assertTrue(ins2.update_indel(snp5)) tests = [ (99, [], (100, False)), (100, [], (99, False)), (199, [], (0, False)), (119, [], (80, False)), (119, [del1], (80, False)), (149, [], (50, False)), (149, [del1], (51, False)), (149, [del2], (52, False)), (159, [], (40, False)), (159, [ins1], (39, False)), (159, [ins2], (37, False)), (159, [del1, ins1], (40, False)), (159, [del1, ins2], (38, False)), (159, [del2, ins1], (41, False)), (159, [del2, ins2], (39, False)), (139, [del1], (39, True)), (139, [snp0], (60, False)), (149, [ins1], (49, True)), ] for ref_coord, variant_list, expected in tests: got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) # if we reverse the direction of hit in query and reference, should get the same answer aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start got = aln.qry_coords_from_ref_coord(ref_coord, variant_list) self.assertEqual(expected, got) aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start def test_qry_coords_from_ref_coord_when_variant_not_in_nucmer_match(self): """Test ref_coords_from_qry_coord when variant not in nucmer match""" aln = alignment.Alignment( "1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry" ) snp0 = snp.Snp("127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry") indel = variant.Variant(snp0) self.assertEqual((595, False), aln.qry_coords_from_ref_coord(0, [])) self.assertEqual((595, False), aln.qry_coords_from_ref_coord(0, [indel])) self.assertEqual((995, False), aln.qry_coords_from_ref_coord(400, [])) self.assertEqual((995, False), aln.qry_coords_from_ref_coord(400, [indel])) self.assertEqual((1200, False), aln.qry_coords_from_ref_coord(605, [])) self.assertEqual((1200, False), aln.qry_coords_from_ref_coord(605, [indel])) def test_ref_coords_from_qry_coord_test_same_strand(self): """Test ref_coords_from_qry_coord on same strand""" aln = alignment.Alignment( "\t".join( [ "1", "101", "100", "200", "100", "100", "100.00", "300", "300", "1", "1", "ref", "qry", ] ) ) snp0 = snp.Snp( "\t".join( ["40", "T", "A", "140", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # snp snp0 = variant.Variant(snp0) snp1 = snp.Snp( "\t".join( ["40", ".", "A", "140", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref snp2 = snp.Snp( "\t".join( ["40", ".", "C", "141", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from ref del1 = variant.Variant(snp1) del2 = variant.Variant(snp1) self.assertTrue(del2.update_indel(snp2)) snp3 = snp.Snp( "\t".join( ["50", "A", ".", "150", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry snp4 = snp.Snp( "\t".join( ["51", "C", ".", "150", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry snp5 = snp.Snp( "\t".join( ["52", "G", ".", "150", "x", "x", "300", "300", "x", "1", "ref", "qry"] ) ) # del from qry ins1 = variant.Variant(snp3) ins2 = variant.Variant(snp3) self.assertTrue(ins2.update_indel(snp4)) self.assertTrue(ins2.update_indel(snp5)) tests = [ (99, [], (0, False)), (100, [], (1, False)), (199, [], (100, False)), (119, [del1], (20, False)), (149, [], (50, False)), (149, [del1], (49, False)), (149, [del2], (48, False)), (159, [], (60, False)), (159, [ins1], (61, False)), (159, [ins2], (63, False)), (159, [del1, ins1], (60, False)), (159, [del1, ins2], (62, False)), (159, [del2, ins1], (59, False)), (159, [del2, ins2], (61, False)), (139, [del1], (39, True)), (139, [snp0], (40, False)), (149, [ins1], (49, True)), ] for qry_coord, variant_list, expected in tests: got = aln.ref_coords_from_qry_coord(qry_coord, variant_list) self.assertEqual(expected, got) # if we reverse the direction of hit in query and qryerence, should get the same answer aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start got = aln.ref_coords_from_qry_coord(qry_coord, variant_list) self.assertEqual(expected, got) aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start def test_ref_coords_from_qry_coord_when_variant_not_in_nucmer_match(self): """Test ref_coords_from_qry_coord when variant not in nucmer match""" aln = alignment.Alignment( "1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry" ) snp0 = snp.Snp("127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry") indel = variant.Variant(snp0) self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [])) self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [indel])) self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [])) self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [indel])) self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [])) self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [indel]))