Hello all,
I’m a beginner level python user experiencing a problem using biopython. I’m taking an online bioinformatics course and the example that we’re working through right now is to take a fasta file (called myseq.fa in the following example), open it then read. Then using the NCBIWWW module we need to do a BLAST nt search using the single fasta sequence in the myseq.fa file. However when I do this I get a series of lines in return, some with error messages. I’m including everything below. Does any of this make sense? Any thoughts on how I can fix this?
>>> from Bio.Blast import NCBIWWW
>>> fasta_string = open("myseq.fa").read()
>>> result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1319, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1230, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1276, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1225, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1004, in _send_output
self.send(msg)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 944, in send
self.connect()
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1399, in connect
self.sock = self._context.wrap_socket(self.sock,
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 1040, in _create
self.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 1309, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/Bio/Blast/NCBIWWW.py", line 171, in qblast
handle = _urlopen(request)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1362, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1322, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108)>
>>>
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