[Biopython-dev] 1.62b test coverage report

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 2 09:31:27 UTC 2013

Thanks for these details Ben - it sounds like a mixture of real
test failures, and mere warnings that an external tool wasn't

On Fri, Aug 2, 2013 at 3:20 AM, Ben Fulton <ben at benfulton.net> wrote:
> My test machine was running Ubuntu 12.04.
> For fasttree I installed version 2.1.4-1~ubuntu12.04.1 using apt-get, and
> got this error:
> ApplicationError: Command 'fasttree -out temp_test.tree
> Quality/example.fasta' returned non-zero exit status 1, 'Unknown or
> incorrect use of option -out'

I don't seem to have fasttree installed at all, and from the
test and wrapper it is not explicit about which version is
was originally written for.

> The NCBI_BLAST error involves rpsblast not being in the install.
> Version 2.2.25-7 using apt-get.

I believe this is down to an NCBI stupidity with binary name
clashes, both the old 'legacy' C BLAST and the new C++
BLAST+ suite have a binary called rpsblast.

Our test code copes with this by searching the path and checking
each rpsblast binary found - looking for the new version only.

However, Debian policy is to resolve ambiguities like this with
a unilateral renaming - in this case I *think* they called the new
binary rpsblast+ instead. Can you confirm that? I don't have
access to a Debian machine right now.

So, strictly speaking the Biopython test is correct - you don't
have the new rpsblast installed. However, it would be more
helpful if we also checked for the Debian alias rpsblast+ too.

That shouldn't be too complicated to do - especially if you
could rerun the tests using Biopython from git for me?

> Dialign is version 2.2.1-5 using apt-get. I got two errors: first,
> DIALIGN2_DIR not being set. It was installed to /usr/bin so I set
> DIALIGN2_DIR to that directory; then I got "Environment variable
> DIALIGN2_DIR directory missing BLOSUM file." I'm not sure either of these
> items are needed, though I may have missed them in the documentation.

This again looks like a Debian packaging issue versus the
manual install instructions for Dialign. Perhaps they have
fixed Dialign to find its matrix under a data folder...

You could try simple commenting out the check on the
environment variable in test_Dialign_tool.py and seeing
if the tests pass or not.

> I downloaded version 130708 of Prank from
> http://code.google.com/p/prank-msa/downloads/list. The error is on line 165
> of the test file:
> AssertionError:
> -----------------
>  PRANK v.130708:
> -----------------
> Input for the analysis
>  - converting 'Quality/example.fasta' to 'temp with space.phy'

This sounds like a minor change in the stdout with recent
versions of PRANK.

> EmbossPhylipNew I tried to install from source, but it was complicated and I
> didn't get it finished.
> I'll send some notes on the other errors when I get a few minutes.



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