[Biopython] installing biopython1.53 failed

[Brad Chapman]

Xiang;

> I was trying to install biopython1.53 source on my computer whose OS is Ubuntu according to the installation instructions on biopython wiki, and when I input "python setup.py test" I got failure messages as follows:
> 
> ======================================================================
> FAIL: seqmatchall with pair output piped to stdout.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "test_Emboss.py", line 661, in test_seqtmatchall_piped
>     self.assertEqual(align.get_alignment_length(), 9)
> AssertionError: 471 != 9
> ----------------------------------------------------------------------
> Ran 140 tests in 102.013 seconds
> FAILED (failures = 1)
> 
> Could you help me to figure out what's the problem? Thanks.

Biopython appears to be installed okay, and this is an issue with
parsing EMBOSS output from the program seqmatchall. If you aren't
planning on using EMBOSS, then you can go ahead and use the rest of
Biopython without any worries.

To figure out the issue, it would be useful to know the version of
EMBOSS you are using:

% embossversion
Writes the current EMBOSS version number to a file
6.0.1

If it's an older one, a simple fix may be to upgrade. You should be
able to run 'apt-get update emboss' on ubuntu:

http://packages.ubuntu.com/karmic/emboss

Hope this helps,
Brad