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biopython test failed

I'm trying to install biopython on ubuntu.

(After I've installed all the requirements) I ran these commands in terminal:

python setup.py build
python setup.py test

and I get this error:

FAIL: test_orchid_est (test_NCBI_qblast.TestQblast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/media/userlab/localData/Moriah/biopython-1.65/Tests/test_NCBI_qblast.py", line 69, in test_orchid_est
    0.0000001, None, ["21554275", "18409071", "296087288"])
  File "/media/userlab/localData/Moriah/biopython-1.65/Tests/test_NCBI_qblast.py", line 124, in run_qblast
    % ", ".join(expected_hits)
AssertionError: Missing all of 21554275, 18409071, 296087288 in alignments**

----------------------------------------------------------------------
Ran 1 test in 446.997 seconds

What should I do to fix it?

Thanks

software-error biopython
• 3,646 views • link
updated by Ram Ram • written by moran.an • moran.an

2 answers

In this case it was a harmless failure due to the NCBI BLAST database changing enough over time that the hits we were checking for no longer appeared in the top BLAST hits. This has been fixed by updating the test:

https://github.com/biopython/biopython/commit/08c72f8778a87701586a03dffcce33c7589bc6d7

You can update your Biopython if you want, but I would just ignore it.

• 0 views • link
written by Peter Peter

thanks a lot, solved the problem.

• 0 views • link
written by moran.an • moran.an

If you have root access, then easiest way to install biopython on ubuntu is using package manager.

Simply run:

sudo apt-get install python-biopython

It should install all packages/dependencies.

• 0 views • link
updated by Ram Ram • written by arnstrm arnstrm

I did it before. It's not solving my problem.

• 0 views • link
updated by Ram Ram • written by moran.an • moran.an

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