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When I try to run a test file provided by Biopython for NCBIWWW.qblast online search, it just hangs on and on and never responds. The same happens when I am trying to run any script on my own that includes NCBIWWW.qblast: it just arrives to this line and stalls. No error message is ever issued, no results is ever received and the process never ends in any way.

One of the scripts that produce the problem is this one:

from Bio.Blast import NCBIWWW
result_handle=qblast('blastn', 'nt', 'AGAAAGGGTATATAAAATCAAGAATCTGGGGTGTTTGTGTTGACTTGTATAATTCTTGATTTTTTCAGGTAGTTGAAAAGGTGGGAGAAAAGTGGAGAAGCCTAAGCTGATATTGAAATTCATATGGATGGAAGAACATTGGTTTAGGATTGGATCAAAAAATAGGTGGACATGGAACTGTA')

What can be the issue?

09stephenb
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user3437828
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1 Answers1

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That's totally wrong. It might be the case that your internet connection was lost or the server was too slow to respond. For any NCBI query search, it takes few moments to give you the respond. I got the response pretty fast, try again with a small change, it should work fine for you too:

>>> from Bio.Blast import NCBIWWW
>>> result_handle=NCBIWWW.qblast('blastn', 'nt', 'AGAAAGGGTATATAAAATCAAGAATCTGGGGTGTTTGTGTTGACTTGTATAATTCTTGATTTTTTCAGGTAGTTGAAAAGGTGGGAGAAAAGTGGAGAAGCCTAAGCTGATATTGAAATTCATATGGATGGAAGAACATTGGTTTAGGATTGGATCAAAAAATAGGTGGACATGGAACTGTA')
>>> result_handle
<cStringIO.StringI object at 0x7f3b3cad6718>

It should return you an object to work on!

Sharif Mamun
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