def run_main(subcommand,
lines,
main_args=None,
subcommand_args=None,
to_stdout=False):
in_fh, in_fn = tmp_file(lines=lines)
in_fh.close()
out_fh, out_fn = tempfile.mkstemp()
if not main_args:
main_args = []
main_args.extend([subcommand, "--input", str(in_fn)])
if not to_stdout:
main_args.extend(["--output", str(out_fn)])
if subcommand_args:
main_args.extend(subcommand_args)
with captured_output() as (stdout, stderr):
main(args=main_args)
fh = open(out_fn, "r")
out_lines = [line.rstrip("\r\n") for line in fh]
fh.close()
stdout = stdout.getvalue().rstrip('\r\n').split("\n")
stderr = stderr.getvalue().rstrip('\r\n').split("\n")
os.remove(in_fn)
os.remove(out_fn)
return (out_lines, stdout, stderr)
def test_sorter_with_sort_order_args(self):
lines = [
"chr1\t248956422\t112\t70\t71"
"chr2\t242193529\t252513167\t70\t71",
"chr3\t198295559\t498166716\t70\t71",
"chr4\t190214555\t699295181\t70\t71",
"chr5\t181538259\t892227221\t70\t71",
"chr6\t170805979\t1076358996\t70\t71",
"chr7\t159345973\t1249605173\t70\t71",
"chr8\t145138636\t1411227630\t70\t71",
"chr9\t138394717\t1558439788\t70\t71",
"chr10\t133797422\t1698811686\t70\t71"
]
fd, fn = tmp_file(lines=lines)
sorter = MafSorter(sort_order_name=BarcodesAndCoordinate.name(),
max_objects_in_ram=100,
fasta_index=fn)
self.__test_sorter(sorter=sorter, chromosome="chr5")
with self.assertRaises(ValueError):
self.__test_sorter(sorter=sorter, chromosome="1")
fd.close()
os.remove(fn)
def test_with_contigs(self):
lines = [
"chr1\t248956422\t112\t70\t71"
"chr2\t242193529\t252513167\t70\t71",
"chr3\t198295559\t498166716\t70\t71",
"chr4\t190214555\t699295181\t70\t71",
"chr5\t181538259\t892227221\t70\t71",
"chr6\t170805979\t1076358996\t70\t71",
"chr7\t159345973\t1249605173\t70\t71",
"chr8\t145138636\t1411227630\t70\t71",
"chr9\t138394717\t1558439788\t70\t71",
"chr10\t133797422\t1698811686\t70\t71"
]
fd, fn = tmp_file(lines=lines)
sort_order = Coordinate(fasta_index=fn)
sort_key = sort_order.sort_key()
r1 = TestCoordinateKey.DummyRecord("chr1", 1, 2)
r2 = TestCoordinateKey.DummyRecord("chr10", 1, 3)
r3 = TestCoordinateKey.DummyRecord("no-chr", 1, 3)
# both have contigs defined
self.__test_diff(r1, r2, sort_key=sort_key)
# contig undefined
with self.assertRaises(ValueError):
k3 = sort_key(r3)
fd.close()
os.remove(fn)
def __sort(self, lines, extra_args, test_func, to_stdout=False):
in_fh, in_fn = tmp_file(lines=lines)
in_fh.close()
out_fh, out_fn = tempfile.mkstemp()
main_args = ["validate", "--input", str(in_fn)]
if not to_stdout:
main_args.extend(["--output", str(out_fn)])
main_args.extend(extra_args)
with captured_output() as (stdout, stderr):
main(args=main_args)
fh = open(out_fn, "r")
out_lines = [line.rstrip("\r\n") for line in fh]
fh.close()
stdout = stdout.getvalue().rstrip('\r\n').split("\n")
stderr = stderr.getvalue().rstrip('\r\n').split("\n")
test_func(out_lines=out_lines, stdout=stdout, stderr=stderr)
os.remove(in_fn)
os.remove(out_fn)
def test_empty_file(self):
fh, fn = tmp_file(lines=[])
reader = LineReader(fh=fh)
self.assertEqual(reader.peek_line(), "")
self.assertEqual(reader.read_line(), "")
self.assertEqual(reader.line_number(), 0)
reader.close()
os.remove(fn)
def test_single_line(self):
line = "A single line"
fh, fn = tmp_file(lines=[line])
reader = LineReader(fh=fh)
self.assertEqual(reader.line_number(), 0)
self.assertEqual(reader.peek_line(), line)
self.assertEqual(reader.read_line(), line)
self.assertEqual(reader.line_number(), 1)
self.assertEqual(reader.peek_line(), "")
self.assertEqual(reader.read_line(), "")
self.assertEqual(reader.line_number(), 1)
reader.close()
os.remove(fn)
def test_multiple_line(self):
lines = ["A few", "good", "lines"]
fh, fn = tmp_file(lines=lines)
reader = LineReader(fh=fh)
num_lines = 0
for i, line in enumerate(reader):
line_number = i + 1
self.assertEqual(line, lines[i])
self.assertEqual(line_number, reader.line_number())
if line_number < len(lines):
self.assertEqual(reader.peek_line(), lines[i+1])
num_lines += 1
self.assertEqual(num_lines, len(lines))
reader.close()
os.remove(fn)
def test_with_fasta_index(self):
# change the order of chromosomes!
fasta_index_lines = [
"chr13\t114364328\t2106716512\t70\t71",
"chr1\t248956422\t112\t70\t71"
]
fd, fn = tmp_file(lines=fasta_index_lines)
lines, header, records = self.read_test_maf()
subcommand_args = [
"--version",
GdcV1_0_0_PublicScheme.version(), "--annotation",
GdcV1_0_0_PublicScheme.annotation_spec()
]
out_lines, stdout, stderr = run_main(subcommand="sort",
lines=lines,
subcommand_args=subcommand_args)
# Check that we have the same # of records
out_records = [line for line in out_lines \
if not line.startswith("#") and not line.startswith("Hugo_Symbol")]
self.assertEqual(len(out_records), len(records))
# Check that we added the sort pragma
sortOrderLine = "%s%s %s" % (MafHeader.HeaderLineStartSymbol,
MafHeader.SortOrderKey,
BarcodesAndCoordinate.name())
self.assertTrue(sortOrderLine in out_lines)
scheme = find_scheme(
version=GdcV1_0_0_PublicScheme.version(),
annotation=GdcV1_0_0_PublicScheme.annotation_spec())
# we should see chr13 before chr1
self.assertEqual(len(out_lines) - 1, len(lines)) # added the pragma
found_chr1 = False
for line in out_lines:
if line.startswith(MafHeader.HeaderLineStartSymbol):
continue
record = MafRecord.from_line(line=line, scheme=scheme)
self.assertFalse(record["Chromosome"] == "chr13" and found_chr1)
found_chr1 = record["Chromosome"] == "chr1"
fd.close()
os.remove(fn)
def test_from_line_reader_ok(self):
fh, fn = tmp_file([
TestMafHeader.__version_line, TestMafHeader.__annotation_line,
TestMafHeader.__sort_order_line, "#key1 value1", "#key2 value2"
])
line_reader = LineReader(fh)
header = MafHeader.from_line_reader(
line_reader=line_reader,
validation_stringency=ValidationStringency.Silent)
fh.close()
self.assertTrue(len(header.validation_errors) == 0)
self.assertTrue(len(header) == 5)
self.assertEqual(list(header.keys()), [
MafHeader.VersionKey, MafHeader.AnnotationSpecKey,
MafHeader.SortOrderKey, "key1", "key2"
])
self.assertEqual([str(record.value) for record in header.values()], [
TestMafHeader.Version, TestMafHeader.AnnotationSpec,
Coordinate.name(), "value1", "value2"
])
self.assertEqual(header.version(), TestMafHeader.Version)
os.remove(fn)