biopython test failed

Question

[moran.an]

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

Answer 1

[Peter]

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.

[moran.an]

thanks a lot, solved the problem.

Answer 2

[arnstrm]

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.

[moran.an]

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