def test_close(self):
"""close() flushes the buffer"""
b = BufferedWriter(self.test_fp, buf_size=2)
b.write("1")
b.close()
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, ["1"])
def _split_along_prefix(self, input_fp, params, jobs_to_start, job_prefix,
output_dir):
""" Split input sequences into sets with identical prefix"""
out_files = []
buffered_handles = {}
prefix_length = params['prefix_length'] or 1
for seq_id, seq in parse_fasta(open(input_fp)):
if (len(seq) < prefix_length):
raise ValueError(
"Prefix length must be equal or longer than sequence.\n" +
" Found seq %s with length %d" % (seq_id, len(seq)))
prefix = seq[:prefix_length]
if (prefix not in buffered_handles):
# never seen this prefix before
out_fp = "%s/%s%s" % (output_dir, job_prefix, prefix)
buffered_handles[prefix] = BufferedWriter(out_fp)
out_files.append(out_fp)
self.prefix_counts[prefix] = 0
self.prefix_counts[prefix] += 1
buffered_handles[prefix].write('>%s\n%s\n' % (seq_id, seq))
# make sure all buffers are closed and flushed
for buf_fh in buffered_handles.itervalues():
buf_fh.close()
remove_files = True
return out_files, remove_files
def test_close(self):
"""close() flushes the buffer"""
b = BufferedWriter(self.test_fp, buf_size=2)
b.write("1")
b.close()
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, ["1"])
def test_write(self):
"""BufferedWriter writes nothing until max buffer reached."""
b = BufferedWriter(self.test_fp, buf_size=2)
b.write("1")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, [])
# still nothing
b.write("2")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, [])
# finally, buffer is flushed
b.write("3")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, ["123"])
def test_write(self):
"""BufferedWriter writes nothing until max buffer reached."""
b = BufferedWriter(self.test_fp, buf_size=2)
b.write("1")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, [])
# still nothing
b.write("2")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, [])
# finally, buffer is flushed
b.write("3")
content = open(self.test_fp, "r").readlines()
self.assertEquals(content, ["123"])
def test_init(self):
"""BufferedWriter constructor works"""
b = BufferedWriter(self.test_fp)
self.assertTrue(exists(self.test_fp))
