def test_verbose_stream(self, mock_open):
""" Test progress reporting fails gracefully on stream of unknown len. """
outfh = StringIO.StringIO()
f_map = {"in.fa": self.file1}
mock_open.side_effect = build_mock_open_side_effect(f_map)
with mock.patch('sys.stderr', outfh):
res = "\n".join([s.to_fasta_str(include_coords=False)
for s in fastaIterator("in.fa", verbose=True)])
self.assertEqual("Warning: unable to show progress for stream. Reason:" +
" 'Failed to get max size for stream'",
outfh.getvalue())
self.assertEqual(res.strip(), self.file1.strip())
def testTwoFiles(self, mock_open):
outfh = StringIO.StringIO()
stream_d = {"out.bed": outfh}
mock_open.side_effect = build_mock_open_side_effect(
self.str_d, stream_d)
main(["-o", "out.bed", "file1.bed", "file2.bed"])
expect = "\n".join([
"\t".join(["chr1", "10", "12", "X", "0", "+"]), "\t".join([
"chr1", "75", "80", "X", "0", "+"
]), "\t".join(["chr2", "73", "75", "X", "0", "+"]), "\t".join(
["chr2", "90", "92", "X", "0", "+"])
]) + "\n"
self.assertEqual(outfh.getvalue(), expect)
def setUp(self):
f1_conts = "\n".join(["\t".join(["chr1", "10", "20", "F1_R1", "0", "+"]),
"\t".join(["chr1", "70", "80", "F2_R2", "0", "+"]),
"\t".join(["chr2", "05", "10", "F2_R2", "0", "+"]),
"\t".join(["chr2", "70", "75", "F2_R2", "0", "+"]),
"\t".join(["chr2", "90", "95", "F2_R2", "0", "+"])])
f2_conts = "\n".join(["\t".join(["chr1", "07", "12", "F1_R1", "0", "+"]),
"\t".join(["chr1", "67", "70", "F2_R2", "0", "+"]),
"\t".join(["chr1", "75", "85", "F2_R2", "0", "+"]),
"\t".join(["chr2", "20", "30", "F2_R2", "0", "+"]),
"\t".join(["chr2", "73", "92", "F2_R2", "0", "+"])])
string_d = {"file1.bed": f1_conts,
"file2.bed": f2_conts}
self.mock_open_side_effect = build_mock_open_side_effect(string_d, {})
def test_anchor_start_norm(self, mock_open):
outfh = StringIO.StringIO()
streams = {"out.dat": outfh}
mock_open.side_effect = build_mock_open_side_effect(self.f_map, streams)
_main(["-n", "-o", "out.dat", "regions.bed", "hits1.bed"], sys.argv[0])
expect = [[0, 0.0], [1, 1.0], [2, 0.0], [3, 0.0], [4, 0.0], [5, 0.6667],
[6, 0.0], [7, 0.0], [8, 0.0], [9, 0.0], [10, 0.0], [11, 0.0],
[12, 0.0], [13, 0.0], [14, 0.0], [15, 1.0]]
got = outfh.getvalue()
got = [[float(a) for a in x.split()] for x in got.split("\n")
if x.strip() != ""]
self.assertEqual(len(got), len(expect))
for i in range(0, len(got)):
self.assertEqual(len(got[i]), 2)
self.assertAlmostEqual(got[i][0], expect[i][0])
self.assertAlmostEqual(got[i][1], expect[i][1], places=4)
def testTwoFiles(self, mock_open):
outfh = StringIO.StringIO()
stream_d = {"out.bed": outfh}
mock_open.side_effect = build_mock_open_side_effect(self.str_d, stream_d)
main(["-o", "out.bed", "file1.bed", "file2.bed"])
expect = (
"\n".join(
[
"\t".join(["chr1", "10", "12", "X", "0", "+"]),
"\t".join(["chr1", "75", "80", "X", "0", "+"]),
"\t".join(["chr2", "73", "75", "X", "0", "+"]),
"\t".join(["chr2", "90", "92", "X", "0", "+"]),
]
)
+ "\n"
)
self.assertEqual(outfh.getvalue(), expect)
def setUp(self):
f1_conts = "\n".join([
"\t".join(["chr1", "10", "20", "F1_R1", "0", "+"]),
"\t".join(["chr1", "70", "80", "F2_R2", "0", "+"]),
"\t".join(["chr2", "05", "10", "F2_R2", "0", "+"]),
"\t".join(["chr2", "70", "75", "F2_R2", "0", "+"]),
"\t".join(["chr2", "90", "95", "F2_R2", "0", "+"])
])
f2_conts = "\n".join([
"\t".join(["chr1", "07", "12", "F1_R1", "0", "+"]),
"\t".join(["chr1", "67", "70", "F2_R2", "0", "+"]),
"\t".join(["chr1", "75", "85", "F2_R2", "0", "+"]),
"\t".join(["chr2", "20", "30", "F2_R2", "0", "+"]),
"\t".join(["chr2", "73", "92", "F2_R2", "0", "+"])
])
string_d = {"file1.bed": f1_conts, "file2.bed": f2_conts}
self.mock_open_side_effect = build_mock_open_side_effect(string_d, {})
def test_anchor_start_norm(self, mock_open):
outfh = StringIO.StringIO()
streams = {"out.dat": outfh}
mock_open.side_effect = build_mock_open_side_effect(
self.f_map, streams)
_main(["-n", "-o", "out.dat", "regions.bed", "hits1.bed"], sys.argv[0])
expect = [[0, 0.0], [1, 1.0], [2, 0.0], [3, 0.0], [4,
0.0], [5, 0.6667],
[6, 0.0], [7, 0.0], [8, 0.0], [9, 0.0], [10, 0.0], [11, 0.0],
[12, 0.0], [13, 0.0], [14, 0.0], [15, 1.0]]
got = outfh.getvalue()
got = [[float(a) for a in x.split()] for x in got.split("\n")
if x.strip() != ""]
self.assertEqual(len(got), len(expect))
for i in range(0, len(got)):
self.assertEqual(len(got[i]), 2)
self.assertAlmostEqual(got[i][0], expect[i][0])
self.assertAlmostEqual(got[i][1], expect[i][1], places=4)
def test_basic(self, mock_open):
outfh1 = StringIO.StringIO()
outfh2 = StringIO.StringIO()
streams = {"out1.dat": outfh1, "out2.dat": outfh2}
mock_open.side_effect = build_mock_open_side_effect(self.f_map, streams)
_main(["-f", "sfile1", "-s", "sfile2", "-o", "out1.dat out2.dat"],
sys.argv[0])
expectedOutput1 = "\n".join(["\t".join(["chr1", "1", "2", "read1"]),
"\t".join(["chr2", "3", "4", "read4"]),
"\t".join(["chr4", "3", "3", "read6"])])
expectedOutput2 = "\t".join(["chr1", "3", "4", "read3"])
gotOutput1 = outfh1.getvalue()
gotOutput2 = outfh2.getvalue()
self.assertTrue(gotOutput1 == (expectedOutput1 + "\n"))
self.assertTrue(gotOutput2 == (expectedOutput2 + "\n"))
def test_simple(self, mock_open):
out_strm = StringIO.StringIO()
f = "@700156R:635:C7RW1ACXX:8:1101:1499:2065 2:N:0:41\n" +\
"ACGAC\n" +\
"+\n" +\
"B<<BB\n" +\
"@700156R:635:C7RW1ACXX:8:1101:1421:2159 2:N:0:41\n" +\
"TCGAC\n" +\
"+\n" +\
"<B0BF\n"
f_map = {"in.fq": f}
streams = {"out.dat": out_strm}
mock_open.side_effect = build_mock_open_side_effect(f_map, streams)
_main(["-o", "out.dat", "in.fq"], sys.argv[0])
expect = "\n".join([
"\t".join(["0", "A", "1"]), "\t".join(["0", "T", "1"]),
"\t".join(["1", "C", "2"]), "\t".join(["2", "G", "2"]),
"\t".join(["3", "A", "2"]), "\t".join(["4", "C", "2"])
])
self.assertEqual(expect + "\n", out_strm.getvalue())
def test_basic(self, mock_open):
outfh1 = StringIO.StringIO()
outfh2 = StringIO.StringIO()
streams = {"out1.dat": outfh1, "out2.dat": outfh2}
mock_open.side_effect = build_mock_open_side_effect(
self.f_map, streams)
_main(["-f", "sfile1", "-s", "sfile2", "-o", "out1.dat out2.dat"],
sys.argv[0])
expectedOutput1 = "\n".join([
"\t".join(["chr1", "1", "2",
"read1"]), "\t".join(["chr2", "3", "4", "read4"]),
"\t".join(["chr4", "3", "3", "read6"])
])
expectedOutput2 = "\t".join(["chr1", "3", "4", "read3"])
gotOutput1 = outfh1.getvalue()
gotOutput2 = outfh2.getvalue()
self.assertTrue(gotOutput1 == (expectedOutput1 + "\n"))
self.assertTrue(gotOutput2 == (expectedOutput2 + "\n"))
def test_verbose(self, mock_open, mock_getsize):
""" Test progress reporting works properly """
def mock_get_size_se(*args, **kwargs):
if (args[0] == "in.fa"):
return self.file1_size
else:
raise ValueError("unknown file: " + args[0])
outfh = StringIO.StringIO()
infh = StringIO.StringIO(self.file1)
f_map = {"in.fa": infh}
mock_open.side_effect = build_mock_open_side_effect({}, f_map)
mock_getsize.side_effect = mock_get_size_se
with mock.patch('sys.stderr', outfh):
res = ""
pctngs = []
for s in fastaIterator("in.fa", verbose=True):
res += s.to_fasta_str(include_coords=False)
res += "\n"
pct = math.ceil(100 * infh.tell() / float(self.file1_size))
pctngs.append(" %d%% " % pct)
expect = "\r" + "\r".join(["completed" + m + "of processing in.fa"
for m in pctngs]) + "\n"
self.assertEqual(outfh.getvalue(), expect)
def test_simple(self, mock_open):
out_strm = StringIO.StringIO()
f = "@700156R:635:C7RW1ACXX:8:1101:1499:2065 2:N:0:41\n" +\
"ACGAC\n" +\
"+\n" +\
"B<<BB\n" +\
"@700156R:635:C7RW1ACXX:8:1101:1421:2159 2:N:0:41\n" +\
"TCGAC\n" +\
"+\n" +\
"<B0BF\n"
f_map = {"in.fq": f}
streams = {"out.dat": out_strm}
mock_open.side_effect = build_mock_open_side_effect(f_map, streams)
_main(["-o", "out.dat", "in.fq"], sys.argv[0])
expect = "\n".join(["\t".join(["0", "A", "1"]),
"\t".join(["0", "T", "1"]),
"\t".join(["1", "C", "2"]),
"\t".join(["2", "G", "2"]),
"\t".join(["3", "A", "2"]),
"\t".join(["4", "C", "2"])])
self.assertEqual(expect + "\n", out_strm.getvalue())
