urllib2.HTTPError Python
我有一个带有GI号的文件，想从ncbi中获取FASTA序列.
I have a file with GI numbers and would like to get FASTA sequences from ncbi.
from Bio import Entrez
import time
Entrez.email ="eigtw59tyjrt403@gmail.com"
f = open("C:\\bioinformatics\\gilist.txt")
for line in iter(f):
handle = Entrez.efetch(db="nucleotide", id=line, retmode="xml")
records = Entrez.read(handle)
print ">GI "+line.rstrip()+" "+records[0]["GBSeq_primary-accession"]+" "+records[0]["GBSeq_definition"]+"\n"+records[0]["GBSeq_sequence"]
time.sleep(1) # to make sure not many requests go per second to ncbi
f.close()
此脚本运行正常，但是经过几个序列后，我突然收到此错误消息.
This script runs fine but I suddenly get this error message after a few sequences.
Traceback (most recent call last):
File "C:/Users/Ankur/PycharmProjects/ncbiseq/getncbiSeq.py", line 7, in <module>
handle = Entrez.efetch(db="nucleotide", id=line, retmode="xml")
File "C:\Python27\lib\site-packages\Bio\Entrez\__init__.py", line 139, in efetch
return _open(cgi, variables)
File "C:\Python27\lib\site-packages\Bio\Entrez\__init__.py", line 455, in _open
raise exception
urllib2.HTTPError: HTTP Error 500: Internal Server Error
我当然可以使用http://www.ncbi.nlm.nih.gov/sites/batchentrez，但是我正在尝试创建管道并希望自动化.
Of course I can use http://www.ncbi.nlm.nih.gov/sites/batchentrez but I am trying to create a pipeline and would like something automated.
如何防止ncbi踢我出去"
How can I prevent ncbi from "kicking me out"
这是正常"的Entrez API临时失败，即使您应用了所有Entrez API规则也可能发生. Biopython文档在本节.
It's a "normal" Entrez API temporary fail which can occur even if you've applied all Entrez API rules. Biopython documentation explains a way to handle it in this section.
有时您会从Entrez收到间歇性错误，HTTPError 5XX，我们使用了一个尝试(暂停重试块除外)来解决此问题.例如，
Sometimes you will get intermittent errors from Entrez, HTTPError 5XX, we use a try except pause retry block to address this. For example,
# This assumes you have already run a search as shown above,
# and set the variables count, webenv, query_key
try:
from urllib.error import HTTPError # for Python 3
except ImportError:
from urllib2 import HTTPError # for Python 2
batch_size = 3
out_handle = open("orchid_rpl16.fasta", "w")
for start in range(0, count, batch_size):
end = min(count, start+batch_size)
print("Going to download record %i to %i" % (start+1, end))
attempt = 0
while attempt < 3:
attempt += 1
try:
fetch_handle = Entrez.efetch(db="nucleotide",
rettype="fasta", retmode="text",
retstart=start, retmax=batch_size,
webenv=webenv, query_key=query_key,
idtype="acc")
except HTTPError as err:
if 500 <= err.code <= 599:
print("Received error from server %s" % err)
print("Attempt %i of 3" % attempt)
time.sleep(15)
else:
raise
data = fetch_handle.read()
fetch_handle.close()
out_handle.write(data)
out_handle.close()
因此，您不必为这个错误感到内just，只需抓住它即可.
So you don't to feel guilty about this error and just have to catch it.