def test_writer(header_samples, tmpdir_factory):
O = vcfpy.OrderedDict
# open temporary file and setup the Writer with header
path = tmpdir_factory.mktemp("write_header").join("out.vcf")
header, _ = header_samples
# construct record to write out from scratch
r = record.Record(
"20",
100,
[],
"C",
[record.Substitution(record.SNV, "T")],
None,
[],
O(),
["GT"],
[
record.Call("NA00001", O(GT="0/1")),
record.Call("NA00002", O(GT="0/0")),
record.Call("NA00003", O(GT="1/1")),
],
)
# open writer
with writer.Writer.from_path(path, header) as w:
# write out the record
w.write_record(r)
# should be closed
assert w.stream
assert w.stream.closed
# compare actual result with expected
RESULT = path.read()
LINE = "20\t100\t.\tC\tT\t.\t.\t.\tGT\t0/1\t0/0\t1/1\n"
EXPECTED = MEDIUM_HEADER + LINE
assert EXPECTED == RESULT
def test_write_record_with_escaping(header_samples, tmpdir_factory):
O = vcfpy.OrderedDict
S = record.Substitution
# open temporary file and setup the Writer with header
path = tmpdir_factory.mktemp("write_header").join("out.vcf")
header, _ = header_samples
w = writer.Writer.from_path(path, header)
# construct record to write out from scratch
r = record.Record(
"20",
100,
[],
"C",
[record.Substitution(record.SNV, "T")],
None,
[],
O([("ANNO", ["Here,are%some chars", "%25"])]),
["GT", "FT"],
[
record.Call("NA00001", O(GT="0/1", FT=["%25", "FOO"])),
record.Call("NA00002", O(GT="0/0", FT=[])),
record.Call("NA00003", O(GT="1/1", FT=[])),
],
)
# write out the record, close file to ensure flushing to disk
w.write_record(r)
w.close()
# compare actual result with expected
RESULT = path.read()
LINE = ("20\t100\t.\tC\tT\t.\t.\tANNO=Here%2Care%25some chars,"
"%2525\tGT:FT\t0/1:%2525;FOO\t0/0:.\t1/1:.\n")
EXPECTED = MEDIUM_HEADER + LINE
assert EXPECTED == RESULT
def test_write_annotated_record(header_samples, tmpdir_factory):
O = vcfpy.OrderedDict
S = record.Substitution
# open temporary file and setup the Writer with header
path = tmpdir_factory.mktemp("write_annotated_record").join("out.vcf")
header, _ = header_samples
w = writer.Writer.from_path(path, header)
# construct record to write out from scratch
r = record.Record(
"20",
100,
["rs333", "CSN42"],
"C",
[
record.Substitution(record.SNV, "T"),
record.Substitution(record.SNV, "G")
],
50,
["PASS"],
O([("DP", 93), ("AF", [0.3, 0.2]), ("DB", True)]),
["GT", "DP", "GQ", "HQ"],
[
record.Call("NA00001", O(GT="0/1", DP=30, GQ=40, HQ=[1, 2])),
record.Call("NA00002", O(GT="0/2", DP=31, GQ=41, HQ=[3, 4])),
record.Call("NA00003", O(GT="1/2", DP=32, GQ=42, HQ=[5, 6])),
],
)
# write out the record, close file to ensure flushing to disk
w.write_record(r)
w.close()
# compare actual result with expected
RESULT = path.read()
LINE = "20\t100\trs333;CSN42\tC\tT,G\t50\tPASS\tDP=93;AF=0.3,0.2;DB\tGT:DP:GQ:HQ\t0/1:30:40:1,2\t0/2:31:41:3,4\t1/2:32:42:5,6\n"
EXPECTED = MEDIUM_HEADER + LINE
assert EXPECTED == RESULT
def test_gt_type_het():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0|1")]))
assert call.gt_type == vcfpy.HET
def test_gt_bases_0_2():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0|2")]))
build_rec([call])
assert call.gt_bases == ("C", "A")
def test_gt_bases_1_1():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "1|1")]))
build_rec([call])
assert call.gt_bases == ("T", "T")
def test_gt_phase_char_slash():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0/1")]))
assert call.gt_phase_char == "/"
def test_gt_phase_char_pipe():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0|1")]))
assert call.gt_phase_char == "|"
def test_is_phased_false():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0/1")]))
assert call.is_phased is False
def test_is_het_het():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0|1")]))
assert call.is_het
def test_ploidy_two():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "1/1")]))
assert call.ploidy == 2
def test_gt_type_filtered_no_ft():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "1/1")]))
assert not call.is_filtered()
def test_is_variant_no_call():
call1 = record.Call("sample", vcfpy.OrderedDict([("GT", ".")]))
assert not call1.is_variant
call2 = record.Call("sample", vcfpy.OrderedDict([("GT", "./.")]))
assert not call2.is_variant
def test_is_variant_hom_alt():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "1/1")]))
assert call.is_variant
def test_is_variant_hom_ref():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0/0")]))
assert not call.is_variant
def test_gt_type_hom_ref():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0/0")]))
assert call.gt_type == vcfpy.HOM_REF
def test_is_phased_mixed():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "0/1|2")]))
assert call.is_phased is True
def test_gt_type_filtered_pass():
call = record.Call("sample",
vcfpy.OrderedDict([("GT", "1/1"), ("FT", ["PASS"])]))
assert not call.is_filtered()
def test_gt_type_hom_alt():
call = record.Call("sample", vcfpy.OrderedDict([("GT", "1/1")]))
assert call.gt_type == vcfpy.HOM_ALT
