def test_both_ways(self):
filename = "Roche/E3MFGYR02_random_10_reads.sff"
with open(filename, "rb") as handle:
index1 = sorted(_sff_read_roche_index(handle))
with open(filename, "rb") as handle:
index2 = sorted(_sff_do_slow_index(handle))
self.assertEqual(index1, index2)
with open(filename, "rb") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename, "rb") as handle:
self.assertEqual(len(index1),
len(list(SffIterator(BytesIO(handle.read())))))
if sys.platform != "win32" and sys.version_info[0] < 3:
# Can be lazy and treat as binary...
with open(filename, "r") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename) as handle:
index2 = sorted(_sff_read_roche_index(handle))
self.assertEqual(index1, index2)
with open(filename, "r") as handle:
index2 = sorted(_sff_do_slow_index(handle))
self.assertEqual(index1, index2)
with open(filename, "r") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename, "r") as handle:
self.assertEqual(
len(index1),
len(list(SffIterator(BytesIO(handle.read())))))
def test_both_ways(self):
filename = "Roche/E3MFGYR02_random_10_reads.sff"
with open(filename, "rb") as handle:
index1 = sorted(_sff_read_roche_index(handle))
with open(filename, "rb") as handle:
index2 = sorted(_sff_do_slow_index(handle))
self.assertEqual(index1, index2)
with open(filename, "rb") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename, "rb") as handle:
self.assertEqual(len(index1), len(list(SffIterator(BytesIO(handle.read())))))
if sys.platform != "win32" and sys.version_info[0] < 3:
# Can be lazy and treat as binary...
with open(filename, "r") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename) as handle:
index2 = sorted(_sff_read_roche_index(handle))
self.assertEqual(index1, index2)
with open(filename, "r") as handle:
index2 = sorted(_sff_do_slow_index(handle))
self.assertEqual(index1, index2)
with open(filename, "r") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename, "r") as handle:
self.assertEqual(len(index1), len(list(SffIterator(BytesIO(handle.read())))))
def test_index(self):
filename = "Roche/greek.sff"
with open(filename, "rb") as a_handle, open(filename,
"rb") as b_handle:
index1 = sorted(_sff_read_roche_index(a_handle))
index2 = sorted(_sff_do_slow_index(b_handle))
self.assertEqual(index1, index2)
def test_index(self):
filename = "Roche/greek.sff"
# with open(filename, "rb") as handle:
# for record in SffIterator(handle):
# print(record.id)
with open(filename, "rb") as a_handle, open(filename, "rb") as b_handle:
index1 = sorted(_sff_read_roche_index(a_handle))
index2 = sorted(_sff_do_slow_index(b_handle))
self.assertEqual(index1, index2)
def test_index(self):
filename = "Roche/greek.sff"
# with open(filename, "rb") as handle:
# for record in SffIterator(handle):
# print(record.id)
with open(filename, "rb") as a_handle, open(filename, "rb") as b_handle:
index1 = sorted(_sff_read_roche_index(a_handle))
index2 = sorted(_sff_do_slow_index(b_handle))
self.assertEqual(index1, index2)
def test_both_ways(self):
filename = "Roche/E3MFGYR02_random_10_reads.sff"
with open(filename, "rb") as handle:
index1 = sorted(_sff_read_roche_index(handle))
with open(filename, "rb") as handle:
index2 = sorted(_sff_do_slow_index(handle))
self.assertEqual(index1, index2)
with open(filename, "rb") as handle:
self.assertEqual(len(index1), len(list(SffIterator(handle))))
with open(filename, "rb") as handle:
self.assertEqual(len(index1), len(list(SffIterator(BytesIO(handle.read())))))
w._flow_chars = records[0].annotations["flow_chars"]
w._number_of_flows_per_read = len(w._flow_chars)
w.write_header()
w._index_start = out_handle.tell()
w._index_length = len(index)
out_handle.seek(0)
w.write_header() # this time with index info
w.handle.write(index)
for record in records:
w.write_record(record)
with open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb") as handle:
records2 = list(SffIterator(handle))
for old, new in zip(records, records2):
assert old.seq == new.seq
with open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb") as handle:
i = list(_sff_do_slow_index(handle))
# Ugly bit of code to make a fake index in middle
index = ".diy1.00This is a fake index block (DIY = Do It Yourself), which is allowed under the SFF standard.\0"
padding = len(index) % 8
if padding:
padding = 8 - padding
index += chr(0) * padding
with open("Roche/E3MFGYR02_random_10_reads.sff", "rb") as handle:
records = list(SffIterator(handle))
with open("Roche/E3MFGYR02_alt_index_in_middle.sff", "w") as out_handle:
w = SffWriter(out_handle, index=False, xml=None)
# Fake the header...
w._number_of_reads = len(records)
w._index_start = 0
w._index_length = 0
w._number_of_flows_per_read = len(w._flow_chars)
w.write_header()
w._index_start = out_handle.tell()
w._index_length = len(index)
out_handle.seek(0)
w.write_header() # this time with index info
w.handle.write(index)
for record in records:
w.write_record(record)
out_handle.close()
records2 = list(
SffIterator(open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb")))
for old, new in zip(records, records2):
assert str(old.seq) == str(new.seq)
i = list(
_sff_do_slow_index(open("Roche/E3MFGYR02_alt_index_at_start.sff",
"rb")))
# Ugly bit of code to make a fake index in middle
records = list(
SffIterator(open("Roche/E3MFGYR02_random_10_reads.sff", "rb")))
out_handle = open("Roche/E3MFGYR02_alt_index_in_middle.sff", "w")
index = ".diy1.00This is a fake index block (DIY = Do It Yourself), which is allowed under the SFF standard.\0"
padding = len(index) % 8
if padding:
padding = 8 - padding
index += chr(0) * padding
w = SffWriter(out_handle, index=False, xml=None)
# Fake the header...
w._number_of_reads = len(records)
w._index_start = 0
w._index_length = 0
w._flow_chars = records[0].annotations["flow_chars"]
w._number_of_flows_per_read = len(w._flow_chars)
w.write_header()
w._index_start = out_handle.tell()
w._index_length = len(index)
out_handle.seek(0)
w.write_header() # this time with index info
w.handle.write(index)
for record in records:
w.write_record(record)
out_handle.close()
records2 = list(SffIterator(
open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb")))
for old, new in zip(records, records2):
assert str(old.seq) == str(new.seq)
i = list(_sff_do_slow_index(
open("Roche/E3MFGYR02_alt_index_at_start.sff", "rb")))
# Ugly bit of code to make a fake index in middle
records = list(SffIterator(
open("Roche/E3MFGYR02_random_10_reads.sff", "rb")))
out_handle = open(
"Roche/E3MFGYR02_alt_index_in_middle.sff", "w")
index = ".diy1.00This is a fake index block (DIY = Do It Yourself), which is allowed under the SFF standard.\0"
padding = len(index) % 8
if padding:
padding = 8 - padding
index += chr(0) * padding
w = SffWriter(out_handle, index=False, xml=None)
# Fake the header...
w._number_of_reads = len(records)
w._index_start = 0