I have a list of around 200 plastid genomes which I want to download from genbank using biopython, and then put into one .gb file.
Here is the code I am using to do this:
out_handle = open(filename, "w")
for i in range(len(genbankIDs)):
net_handle = Entrez.efetch(
db="nucleotide", id=genbankIDs[i], rettype="gbwithparts", retmode="text"
)
out_handle.write(net_handle.read())
out_handle.close()
net_handle.close()
print("Saved")
where genbankIDs is the list of accession numbers of the sequences I want to download from genbank.
However, this only works for the first 20 accessions. I get this error message:
Traceback (most recent call last):
File "fetchFromGenbank.py", line 25, in <module>
db="nucleotide", id=genbankIDs[i], rettype="gbwithparts", retmode="text"
File "/opt/anaconda2/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 195, in efetch
return _open(cgi, variables, post=post)
File "/opt/anaconda2/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 564, in _open
and exception.status // 100 == 4:
AttributeError: 'HTTPError' object has no attribute 'status'
How can I solve this? Is it an instance of NCBI timing out, or a problem based on me using python 2.7 and not a more recent version?
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Wilber0x •
Have you signed up for NCBI_API_KEY? If not you should do that first. Since you are doing this via a script build in a delay between your queries to ensure you don't get flagged by NCBI server for sending too many queries in a short time.
I have built in a time delay upon your suggestion so only one query is submitted per second. This improves the number of sequences downloaded to 140, but still results in the same error message.
I have tried increasing the delay to 60s, and got the same number downloaded as when I used a 1.5s delay. Perhaps I should just do it in batches of 140 rather than all at once.
I used an Entrez API key, and have incorporated delays into my script. Whether the delay is 1.5s or 60s between requests, I still get the same error after 150 plastid genomes.
This was the problem, thanks for the help!
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Wilber0x : Biostars built-in SPAM protection (we need to have this in place sorry) does not allow HTTP links in title (I think it was interpreting HTTPerror in your post title as a link). I have edited that out so hopefully you post will not be automatically flagged/deleted as SPAM now. I also reinstated your account so you should be able to respond.
Thank you for your help