def test_read_pair_iterator_in_error_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# If walks like an iterator and quacks like an iterator...
rpi = rparser.iter_read_pairs()
assert "__iter__" in dir(rpi)
assert "next" in dir(rpi)
# Are the alleged pairs actually pairs?
read_pairs_1 = []
for read_1, read_2 in rpi:
read_pairs_1.append([read_1, read_2])
assert read_1.name[: 19] == read_2.name[: 19]
# Reload parser.
# Note: No 'rewind' or 'reset' capability at the time of this writing.
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# Ensure that error mode is the default mode.
read_pairs_2 = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
matches = \
map(
lambda rp1, rp2: rp1[0].name == rp2[0].name,
read_pairs_1, read_pairs_2
)
assert all(matches) # Assert ALL the matches. :-]
def test_read_pair_iterator_in_error_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# If walks like an iterator and quacks like an iterator...
rpi = rparser.iter_read_pairs()
assert "__iter__" in dir(rpi)
assert "next" in dir(rpi)
# Are the alleged pairs actually pairs?
read_pairs_1 = []
for read_1, read_2 in rpi:
read_pairs_1.append([read_1, read_2])
assert read_1.name[:19] == read_2.name[:19]
# Reload parser.
# Note: No 'rewind' or 'reset' capability at the time of this writing.
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# Ensure that error mode is the default mode.
read_pairs_2 = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
matches = \
map(
lambda rp1, rp2: rp1[0].name == rp2[0].name,
read_pairs_1, read_pairs_2
)
assert all(matches) # Assert ALL the matches. :-]
def test_bzip2_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
for read in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except IOError, err:
print str(err)
def test_iternext():
rparser = ReadParser(utils.get_test_data("fakelump.fa.stoptags.txt"))
read_pairs = []
try:
for read_1, read_2 in rparser.iter_read_pairs():
read_pairs.append(read_1, read_2)
assert 0, "Shouldn't be able to iterate over non FASTA file"
except IOError, err:
print str(err)
def test_iternext():
rparser = ReadParser(utils.get_test_data("fakelump.fa.stoptags.txt"))
read_pairs = []
try:
for read_1, read_2 in rparser.iter_read_pairs():
read_pairs.append(read_1, read_2)
assert 0, "Shouldn't be able to iterate over non FASTA file"
except IOError, err:
print str(err)
def test_bzip2_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
for read in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except IOError as err:
print str(err)
def test_gzip_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
for read in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_read_pair_iterator_in_error_mode_xfail( ):
rparser = \
ReadParser( utils.get_test_data( "test-abund-read-impaired.fa" ) )
failed = True
try:
for rpair in rparser.iter_read_pairs( ): pass
failed = False
except IOError as exc: pass
assert failed
def test_gzip_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
for _ in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_read_pair_iterator_in_ignore_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
read_pairs = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_IGNORE_UNPAIRED):
read_pairs.append([read_1, read_2])
assert read_1.name[:19] == read_2.name[:19]
assert 2 == len(read_pairs)
def test_read_pair_iterator_in_ignore_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
read_pairs = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_IGNORE_UNPAIRED):
read_pairs.append([read_1, read_2])
assert read_1.name[: 19] == read_2.name[: 19]
assert 2 == len(read_pairs)
def test_read_pair_iterator_in_error_mode_xfail():
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
failed = True
try:
for rpair in rparser.iter_read_pairs():
pass
failed = False
except IOError as exc:
pass
assert failed
def test_read_pair_iterator_in_error_mode_xfail():
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
failed = True
try:
for rpair in rparser.iter_read_pairs():
pass
failed = False
except ValueError as exc:
assert "Invalid read pair" in str(exc), str(exc)
assert failed
def test_read_pair_iterator_in_error_mode_xfail():
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
failed = True
try:
for _ in rparser.iter_read_pairs():
pass
failed = False
except ValueError as exc:
assert "Invalid read pair" in str(exc), str(exc)
assert failed
