def fetchFasta(acc, end):
sleep = 0
while True:
fasta = ''
defline = None
sleep += 1
try:
for line in EUtils.fasta(acc):
if line.startswith(">"):
if defline == None:
defline = line
else:
break
else:
fasta += line
if defline != None:
if end <= len(fasta):
return (defline, fasta)
msg = "got truncated response for {}; retrying in a moment".format(acc)
else:
msg = "got no response for {}; retrying in a moment".format(acc)
except KeyboardInterrupt:
sys.stderr.write(" cancelled\n")
exit(0)
except:
msg = "error fetching {}; retrying in a moment".format(acc)
pass
if sleep > 10:
sys.stderr.write(" too many retries; try again later.\n")
exit(1)
sys.stderr.write(msg)
sys.stderr.flush()
time.sleep(sleep)
sys.stderr.write("\033[{}D\033[K".format(len(msg)))
sys.stderr.flush()
def getSummary(acc):
while True:
summary = EUtils.summary(acc)
if summary:
return summary