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|
"""
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
|
