def iterate_chunks(fw):
cmtreg = re.compile(r'>[^>]*?\n')
headpos = 0
while True:
chunk = fw.read(2**20)
if not chunk:
break
for mat in cmtreg.finditer(chunk):
if mat.start() != headpos:
seq = chunk[headpos:mat.start()]
yield remove_whitespaces(seq)
yield mat.group().strip()
headpos = mat.end()
seq = chunk[headpos:]
yield remove_whitespaces(seq)
def read(infile):
try:
fw = streaming.FileWrapper(infile, "r")
except IOError:
respath = locate_submat(infile.lower())
fw = streaming.FileWrapper(respath, "r")
with fw:
fw_lines = (l.strip() for l in fw.file)
ichars = []
jstring = None
jsize = 0
scores = []
for line in fw_lines:
if line and not line.startswith("#"):
jstring = remove_whitespaces(line)
jsize = len(jstring) + 1
break
if jstring is None:
raise ValueError("this sub matrix file is broken")
for line in fw.file:
items = line.split()
if not items:
continue
if len(items) != jsize:
raise ValueError("this sub matrix file is broken")
ichars.append(items[0])
scores.append([int(s) for s in items[1:]])
istring = "".join(ichars)
submatr = np.array(scores, dtype=int)
return istring, jstring, submatr
