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"""
Tests for `bx.align.maf.sitemask`.
"""
import tempfile
from io import StringIO
import bx.align.maf
from bx.align.sitemask import cpg
test_maf_cpg = """##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
"""
cpg_inclusive_result = [
"##maf,version=1",
"a,score=0",
"s,apple,34,64,+,110,AGGGA---GTTCGTCACT------GT##TAAGGGTTCAGA--CTGTCTATGTATACACAAGTTGTGTTGCA--ACCG",
"s,orange,19,61,-,100,AGGGATG#GTT--TCACTGCTAT#GT##TA----TTCAGACTTCG-CTATCT------GAGTTGT---GCATTACCG",
]
cpg_restricted_result = [
"##maf,version=1",
"a,score=0",
"s,apple,34,64,+,110,A##GA---#TT##TC#C#------#T##TA###GTTC#GA--C##TC#A#G#ATAC####GT#G#GT#GC#--AC#G",
"s,orange,19,61,-,100,A##GA#G##TT--TC#C#GC#AT##T##TA----TTC#GAC#T##-C#A#C#------##GT#G#---GC#TTAC#G",
]
noncpg_result = [
"##maf,version=1",
"a,score=0",
"s,apple,34,64,+,110,#GG##---G##CG##A#T------G#CG##AGG####A##--#TG##T#T#T####ACAA##T#T##T##A--##CG",
"s,orange,19,61,-,100,#GG##T#CG##--##A#T##T##CG#CG##----###A###T#CG-#T#T#T------GA##T#T---##A####CG",
]
def test_cpg_inclusive():
reader = bx.align.maf.Reader(StringIO(test_maf_cpg))
out = tempfile.NamedTemporaryFile("w")
writer = bx.align.maf.Writer(out)
cpgfilter = cpg.Inclusive(mask="#")
cpgfilter.run(reader, writer.write)
out.seek(0)
j = 0
for line in open(out.name):
line = line.strip()
if not (line):
continue
assert cpg_inclusive_result[j] == ",".join(line.split())
j += 1
def test_cpg_restricted():
reader = bx.align.maf.Reader(StringIO(test_maf_cpg))
out = tempfile.NamedTemporaryFile("w")
writer = bx.align.maf.Writer(out)
cpgfilter = cpg.Restricted(mask="#")
cpgfilter.run(reader, writer.write)
out.seek(0)
j = 0
for line in open(out.name):
line = line.strip()
if not (line):
continue
assert cpg_restricted_result[j] == ",".join(line.split())
j += 1
def test_non_cpg():
reader = bx.align.maf.Reader(StringIO(test_maf_cpg))
out = tempfile.NamedTemporaryFile("w")
writer = bx.align.maf.Writer(out)
cpgfilter = cpg.nonCpG(mask="#")
cpgfilter.run(reader, writer.write)
out.seek(0)
j = 0
for line in open(out.name):
line = line.strip()
if not (line):
continue
assert noncpg_result[j] == ",".join(line.split())
j += 1
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