def test_add_flag():
vcf = VCF(VCF_PATH)
vcf.add_info_to_header({'ID': 'myflag', 'Description': 'myflag',
'Type':'Flag', 'Number': '0'})
# NOTE that we have to add the info to the header of the reader,
# not the writer because the record will be associated with the reader
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, vcf)
rec = vcf.next()
rec.INFO["myflag"] = True
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.INFO["myflag"] is None, dict(v.INFO)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, vcf)
rec.INFO["myflag"] = False
w.write_record(rec)
v = next(VCF(f))
assert_raises(KeyError, v.INFO.__getitem__, "myflag")
def test_add_flag():
vcf = VCF(VCF_PATH)
vcf.add_info_to_header({
'ID': 'myflag',
'Description': 'myflag',
'Type': 'Flag',
'Number': '0'
})
# NOTE that we have to add the info to the header of the reader,
# not the writer because the record will be associated with the reader
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, vcf)
rec = vcf.next()
rec.INFO["myflag"] = True
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.INFO["myflag"] is None, dict(v.INFO)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, vcf)
rec.INFO["myflag"] = False
w.write_record(rec)
v = next(VCF(f))
assert_raises(KeyError, v.INFO.__getitem__, "myflag")
def test_add_filter_to_header():
v = VCF(VCF_PATH)
# NOTE that we have to add the filter to the header of the reader,
# not the writer because the record will be associated with the reader
v.add_filter_to_header({'ID': 'abcdefg', 'Description': 'abcdefg'})
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, v)
rec = v.next()
rec.FILTER = ["abcdefg"]
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.FILTER == "abcdefg", v.FILTER
def test_add_filter_to_header():
v = VCF(VCF_PATH)
# NOTE that we have to add the filter to the header of the reader,
# not the writer because the record will be associated with the reader
v.add_filter_to_header({'ID': 'abcdefg', 'Description': 'abcdefg'})
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, v)
rec = v.next()
rec.FILTER = ["abcdefg"]
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.FILTER == "abcdefg", v.FILTER
def test_add_info_to_header():
v = VCF(VCF_PATH)
v.add_info_to_header({'ID': 'abcdefg', 'Description': 'abcdefg',
'Type':'Character', 'Number': '1'})
# NOTE that we have to add the info to the header of the reader,
# not the writer because the record will be associated with the reader
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, v)
import sys
rec = v.next()
rec.INFO["abcdefg"] = "XXX"
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.INFO["abcdefg"] == "XXX", dict(v.INFO)
def test_add_info_to_header():
v = VCF(VCF_PATH)
v.add_info_to_header({
'ID': 'abcdefg',
'Description': 'abcdefg',
'Type': 'Character',
'Number': '1'
})
# NOTE that we have to add the info to the header of the reader,
# not the writer because the record will be associated with the reader
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
w = Writer(f, v)
import sys
rec = v.next()
rec.INFO["abcdefg"] = "XXX"
w.write_record(rec)
w.close()
v = next(VCF(f))
assert v.INFO["abcdefg"] == "XXX", dict(v.INFO)
def test_writer():
v = VCF(VCF_PATH)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
o = Writer(f, v)
rec = v.next()
rec.INFO["AC"] = "3"
rec.FILTER = ["LowQual"]
o.write_record(rec)
rec.FILTER = ["LowQual", "VQSRTrancheSNP99.90to100.00"]
o.write_record(rec)
rec.FILTER = "PASS"
o.write_record(rec)
o.close()
expected = ["LowQual", "LowQual;VQSRTrancheSNP99.90to100.00", None]
for i, variant in enumerate(VCF(f)):
assert variant.FILTER == expected[i], (variant.FILTER, expected[i])
def test_writer():
v = VCF(VCF_PATH)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
o = Writer(f, v)
rec = v.next()
rec.INFO["AC"] = "3"
rec.FILTER = ["LowQual"]
o.write_record(rec)
rec.FILTER = ["LowQual", "VQSRTrancheSNP99.90to100.00"]
o.write_record(rec)
rec.FILTER = "PASS"
o.write_record(rec)
o.close()
expected = ["LowQual", "LowQual;VQSRTrancheSNP99.90to100.00", None]
for i, variant in enumerate(VCF(f)):
assert variant.FILTER == expected[i], (variant.FILTER, expected[i])
