def convert_Ti_to_FLX(sff_fp, output_fp, use_sfftools=False):
"""Converts Titanium SFF to FLX length reads."""
if use_sfftools:
check_sfffile()
_check_call(['sfffile', '-flx', '-o', output_fp, sff_fp],
stdout=open(os.devnull, 'w'))
else:
header, reads = adjust_sff_cycles(parse_binary_sff(open(sff_fp), True),
100)
write_binary_sff(open(output_fp, 'w'), header, reads)
def convert_Ti_to_FLX(sff_fp, output_fp, use_sfftools=False):
"""Converts Titanium SFF to FLX length reads."""
if use_sfftools:
check_sfffile()
_check_call(
['sfffile', '-flx', '-o', output_fp, sff_fp],
stdout=open(os.devnull, 'w'))
else:
header, reads = adjust_sff_cycles(parse_binary_sff(open(sff_fp), True), 100)
write_binary_sff(open(output_fp, 'w'), header, reads)
def make_per_library_sff(sff_fps, id_list_fp, debug=False):
id_list_basepath, _ = os.path.splitext(id_list_fp)
output_fp = id_list_basepath + '.sff'
sff_datasets = [parse_binary_sff(open(fp), True) for fp in sff_fps]
sff_data = combine_sff_data(*sff_datasets)
ids = parse_id_list(open(id_list_fp))
filtered_sff_data = filter_sff_reads(sff_data, ids_to_keep=ids)
if debug:
print 'Creating SFF file for %s' % id_list_fp
write_binary_sff(open(output_fp, 'w'), *filtered_sff_data)
def make_per_library_sff(sff_fps, id_list_fp, debug=False):
id_list_basepath, _ = os.path.splitext(id_list_fp)
output_fp = id_list_basepath + '.sff'
sff_datasets = [parse_binary_sff(open(fp), True) for fp in sff_fps]
sff_data = combine_sff_data(*sff_datasets)
ids = parse_id_list(open(id_list_fp))
filtered_sff_data = filter_sff_reads(sff_data, ids_to_keep=ids)
if debug:
print 'Creating SFF file for %s' % id_list_fp
write_binary_sff(open(output_fp, 'w'), *filtered_sff_data)
def set_sff_trimpoints(sff_dir, technical_lengths):
"""Set trimpoints to end of technical read for all SFF files in directory.
"""
for lib_id, sff_fp in get_per_lib_sff_fps(sff_dir):
try:
readlength = technical_lengths[lib_id]
except KeyError:
continue
sff_data = parse_binary_sff(open(sff_fp), True)
clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
_, temp_fp = tempfile.mkstemp(dir=sff_dir)
with open(temp_fp, "w") as f:
write_binary_sff(f, clipped_header, clipped_reads)
shutil.move(temp_fp, sff_fp)
def set_sff_trimpoints(sff_dir, technical_lengths):
"""Set trimpoints to end of technical read for all SFF files in directory.
"""
for lib_id, sff_fp in get_per_lib_sff_fps(sff_dir):
try:
readlength = technical_lengths[lib_id]
except KeyError:
continue
sff_data = parse_binary_sff(open(sff_fp), True)
clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
_, temp_fp = tempfile.mkstemp(dir=sff_dir)
with open(temp_fp, 'w') as f:
write_binary_sff(f, clipped_header, clipped_reads)
shutil.move(temp_fp, sff_fp)
def test_write_binary_sff(self):
read = READ_HEADER.copy()
read.update(READ_DATA)
header = COMMON_HEADER.copy()
header['number_of_reads'] = 1
write_binary_sff(self.output_file, header, [read])
file_pos = self.output_file.tell()
self.assertTrue(file_pos % 8 == 0)
self.output_file.seek(0)
observed_header, observed_reads = parse_binary_sff(
self.output_file, native_flowgram_values=True)
observed_reads = list(observed_reads)
self.assertEqual(observed_header, header)
self.assertEqual(observed_reads[0], read)
self.assertEqual(len(observed_reads), 1)
file_pos = self.output_file.tell()
self.assertTrue(file_pos % 8 == 0)
def test_write_binary_sff(self):
read = READ_HEADER.copy()
read.update(READ_DATA)
header = COMMON_HEADER.copy()
header['number_of_reads'] = 1
write_binary_sff(self.output_file, header, [read])
file_pos = self.output_file.tell()
self.assertTrue(file_pos % 8 == 0)
self.output_file.seek(0)
observed_header, observed_reads = parse_binary_sff(
self.output_file, native_flowgram_values=True)
observed_reads = list(observed_reads)
self.assertEqual(observed_header, header)
self.assertEqual(observed_reads[0], read)
self.assertEqual(len(observed_reads), 1)
file_pos = self.output_file.tell()
self.assertTrue(file_pos % 8 == 0)