""" Tests for `bx.align.maf`. """ from io import StringIO import bx.align as align import bx.align.maf as maf # A simple MAF from the rat paper days test_maf = """##maf version=1 scoring=humor.v4 # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf # /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf a score=0.128 s human_hoxa 100 8 + 100257 ACA-TTACT s horse_hoxa 120 9 - 98892 ACAATTGCT s fugu_hoxa 88 7 + 90788 ACA--TGCT a score=0.071 s human_unc 9077 8 + 10998 ACAGTATT # Comment s horse_unc 4555 6 - 5099 ACA--ATT s fugu_unc 4000 4 + 4038 AC----TT """ # A more complicated MAF with synteny annotation and such test_maf_2 = """##maf version=1 scoring=autoMZ.v1 a score=3656.000000 s hg17.chr1 2005 34 + 245522847 TGTAACTTAATACCACAACCAGGCATAGGGG--AAA------------- s rheMac2.chr11 9625228 31 + 134511895 TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------ i rheMac2.chr11 C 0 I 1678 s panTro1.chr1 2014 34 + 229575298 TGTAACTTAATACCACAACCAGGCATGGGGG--AAA------------- i panTro1.chr1 C 0 C 0 s bosTau2.chr5 64972365 47 + 76426644 TCCAGCCATGTGTTGTGATCAG--CCAGGGGCTAAAGCCATGGCGGTAG i bosTau2.chr5 C 0 I 1462 s canFam2.chr27 45129665 31 + 48908698 TTTGACTCTGTGCTCTTATCAGGCCCAAGGG------------------ i canFam2.chr27 C 0 I 1664 e danRer3.chr18 2360867 428 + 50308305 I e oryCun1.scaffold_139397 643 1271 - 4771 I e loxAfr1.scaffold_5603 58454 1915 + 68791 I e echTel1.scaffold_212365 4641 1430 + 9822 I e echTel1.scaffold_212365 4641 1430 + 9822 I e rn3.chr4 29161032 1524 - 187371129 I e mm7.chr6 28091695 3290 - 149646834 I """ # A MAF to test slicing upon test_maf_3 = """##maf version=1 scoring=none a score=0 s apple 34 64 + 110 AGGGA---GTTCGTCACT------GTCGTAAGGGTTCAGA--CTGTCTATGTATACACAAGTTGTGTTGCA--ACCG s orange 19 61 - 100 AGGGATGCGTT--TCACTGCTATCGTCGTA----TTCAGACTTCG-CTATCT------GAGTTGT---GCATTACCG """ complex_maf = align.Alignment() complex_maf.score = "7009" complex_maf.components.append( align.Component(src="human_hoxa", start=100, size=8, strand="+", src_size=100257, text="ACA-TTACT") ) complex_maf.components.append( align.Component(src="horse_hoxa", start=120, size=9, strand="-", src_size=98892, text="ACAATTGCT") ) complex_maf.components[-1].synteny_left = (maf.MAF_NEW_STATUS, 0) complex_maf.components[-1].synteny_right = (maf.MAF_CONTIG_STATUS, 0) complex_maf.components.append( align.Component(src="unknown_1", start=150, size=3, strand="-", src_size=98892, text="---ATT---") ) complex_maf.components.append( align.Component(src="unknown_2", start=12, size=1000, strand="+", src_size=1200, text=None) ) complex_maf.components[-1].empty = True complex_maf.components[-1].synteny_empty = maf.MAF_INSERT_STATUS complex_maf.text_size = 9 def test_reader(): reader = maf.Reader(StringIO(test_maf)) assert reader.attributes["version"] == "1" assert reader.attributes["scoring"] == "humor.v4" a = next(reader) assert a.score == 0.128 assert len(a.components) == 3 check_component(a.components[0], "human_hoxa", 100, 8, "+", 100257, "ACA-TTACT") check_component(a.components[1], "horse_hoxa", 120, 9, "-", 98892, "ACAATTGCT") check_component(a.components[2], "fugu_hoxa", 88, 7, "+", 90788, "ACA--TGCT") a = next(reader) assert a.score == 0.071 assert len(a.components) == 3 check_component(a.components[0], "human_unc", 9077, 8, "+", 10998, "ACAGTATT") check_component(a.components[1], "horse_unc", 4555, 6, "-", 5099, "ACA--ATT") check_component(a.components[2], "fugu_unc", 4000, 4, "+", 4038, "AC----TT") a = next(reader) assert a is None reader.close() def test_writer(): val = StringIO() writer = maf.Writer(val, {"scoring": "foobar"}) a = align.Alignment() a.score = 7009 a.components.append( align.Component(src="human_hoxa", start=100, size=9, strand="+", src_size=1000257, text="ACA-TTACT") ) a.components.append( align.Component(src="horse_hoxa", start=120, size=10, strand="-", src_size=98892, text="ACAATTGCT") ) check_component(a.components[0], "human_hoxa", 100, 9, "+", 1000257, "ACA-TTACT") check_component(a.components[1], "horse_hoxa", 120, 10, "-", 98892, "ACAATTGCT") writer.write(a) assert ( val.getvalue() == """##maf version=1 scoring=foobar a score=7009 s human_hoxa 100 9 + 1000257 ACA-TTACT s horse_hoxa 120 10 - 98892 ACAATTGCT """ # noqa: W291 ) def test_slice(): b = complex_maf.slice_by_component(0, 101, 105) check_component(b.components[0], src="human_hoxa", start=101, size=4, strand="+", src_size=100257, text="CA-TT") check_component(b.components[1], src="horse_hoxa", start=121, size=5, strand="-", src_size=98892, text="CAATT") check_component(b.components[2], src="unknown_1", start=150, size=3, strand="-", src_size=98892, text="--ATT") check_component(b.components[3], src="unknown_2", start=12, size=1000, strand="+", src_size=1200, text=None) assert b.components[3].empty assert b.components[3].synteny_empty == maf.MAF_INSERT_STATUS # test slicing with + strand src reader = maf.Reader(StringIO(test_maf_3)) a = next(reader) b = a.slice_by_component(0, 40, 62) check_component( b.components[0], src="apple", start=40, size=22, strand="+", src_size=110, text="TTCGTCACT------GTCGTAAGGGTTC" ) check_component( b.components[1], src="orange", start=28, size=22, strand="-", src_size=100, text="TT--TCACTGCTATCGTCGTA----TTC" ) # test slicing with - strand src b = a.slice_by_component(1, 30, 68) check_component( b.components[0], src="apple", start=46, size=41, strand="+", src_size=110, text="ACT------GTCGTAAGGGTTCAGA--CTGTCTATGTATACACAAGTTG", ) check_component( b.components[1], src="orange", start=32, size=38, strand="-", src_size=100, text="ACTGCTATCGTCGTA----TTCAGACTTCG-CTATCT------GAGTTG", ) a = next(reader) assert a is None def test_reverse_complement(): b = complex_maf.reverse_complement() check_component( b.components[0], src="human_hoxa", start=100257 - 100 - 8, size=8, strand="-", src_size=100257, text="AGTAA-TGT" ) check_component( b.components[1], src="horse_hoxa", start=98892 - 120 - 9, size=9, strand="+", src_size=98892, text="AGCAATTGT" ) assert b.components[1].synteny_right == (maf.MAF_NEW_STATUS, 0) assert b.components[1].synteny_left == (maf.MAF_CONTIG_STATUS, 0) check_component( b.components[2], src="unknown_1", start=98892 - 150 - 3, size=3, strand="+", src_size=98892, text="---AAT---" ) check_component( b.components[3], src="unknown_2", start=1200 - 12 - 1000, size=1000, strand="-", src_size=1200, text=None ) assert b.components[3].empty assert b.components[3].synteny_empty == maf.MAF_INSERT_STATUS def test_column_iter(): expected = [ ["A", "A", "-"], ["C", "C", "-"], ["A", "A", "-"], ["-", "A", "A"], ["T", "T", "T"], ["T", "T", "T"], ["A", "G", "-"], ["C", "C", "-"], ["T", "T", "-"], ] for i, c in enumerate(complex_maf.column_iter()): assert c == expected[i] def test_remove_all_gap_column(): complex_maf_gap = align.Alignment() complex_maf_gap.score = "7009" complex_maf_gap.components.append( align.Component(src="human_hoxa", start=100, size=8, strand="+", src_size=100257, text="-ACA--TTACT") ) complex_maf_gap.components.append( align.Component(src="horse_hoxa", start=120, size=9, strand="-", src_size=98892, text="-ACA-ATTGCT") ) complex_maf_gap.components[-1].synteny_left = (maf.MAF_NEW_STATUS, 0) complex_maf_gap.components[-1].synteny_right = (maf.MAF_CONTIG_STATUS, 0) complex_maf_gap.components.append( align.Component(src="unknown_1", start=150, size=3, strand="-", src_size=98892, text="-----ATT---") ) complex_maf_gap.components.append( align.Component(src="unknown_2", start=12, size=1000, strand="+", src_size=1200, text=None) ) complex_maf_gap.components[-1].empty = True complex_maf_gap.components[-1].synteny_empty = maf.MAF_INSERT_STATUS complex_maf_gap.text_size = 11 complex_maf_gap.remove_all_gap_columns() assert complex_maf_gap == complex_maf def test_read_with_synteny(): reader = maf.Reader(StringIO(test_maf_2), parse_e_rows=True) a = next(reader) check_component( a.components[0], "hg17.chr1", 2005, 34, "+", 245522847, "TGTAACTTAATACCACAACCAGGCATAGGGG--AAA-------------" ) check_component( a.components[1], "rheMac2.chr11", 9625228, 31, "+", 134511895, "TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------", ) print(a.components[1].synteny_left) assert a.components[1].synteny_left == (maf.MAF_CONTIG_STATUS, 0) assert a.components[1].synteny_right == (maf.MAF_INSERT_STATUS, 1678) rat = a.get_component_by_src_start("rn3.") check_component(rat, "rn3.chr4", 29161032, 1524, "-", 187371129, None) assert rat.synteny_empty == maf.MAF_INSERT_STATUS def test_write_with_synteny(): reader = maf.Reader(StringIO(test_maf_2), parse_e_rows=True) a = next(reader) val = StringIO() writer = maf.Writer(val, {"scoring": "foobar"}) writer.write(a) actual = val.getvalue() expected = """##maf version=1 scoring=foobar a score=3656.0 s hg17.chr1 2005 34 + 245522847 TGTAACTTAATACCACAACCAGGCATAGGGG--AAA------------- s rheMac2.chr11 9625228 31 + 134511895 TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------ i rheMac2.chr11 C 0 I 1678 s panTro1.chr1 2014 34 + 229575298 TGTAACTTAATACCACAACCAGGCATGGGGG--AAA------------- i panTro1.chr1 C 0 C 0 s bosTau2.chr5 64972365 47 + 76426644 TCCAGCCATGTGTTGTGATCAG--CCAGGGGCTAAAGCCATGGCGGTAG i bosTau2.chr5 C 0 I 1462 s canFam2.chr27 45129665 31 + 48908698 TTTGACTCTGTGCTCTTATCAGGCCCAAGGG------------------ i canFam2.chr27 C 0 I 1664 e danRer3.chr18 2360867 428 + 50308305 I e oryCun1.scaffold_139397 643 1271 - 4771 I e loxAfr1.scaffold_5603 58454 1915 + 68791 I e echTel1.scaffold_212365 4641 1430 + 9822 I e echTel1.scaffold_212365 4641 1430 + 9822 I e rn3.chr4 29161032 1524 - 187371129 I e mm7.chr6 28091695 3290 - 149646834 I """ # noqa: W291 print(actual) print("---") print(expected) assert actual == expected def check_component(c, src, start, size, strand, src_size, text): assert c.src == src assert c.start == start assert c.size == size assert c.strand == strand assert c.src_size == src_size assert c.text == text