[BioPython] some tests failed

[Brad Chapman]

Hi Dinakar;

> This is my first posting about biopython. I am  newbie to the world of
> python and biopython. Please bear with me.
> I am following the tutorial and cookbook.

Welcome to python and biopython!

> This evening I downloaded biopython code and installed it. python
> setup.py install. It went well and then went and did br_regrtest
> I got the following messages about various test. I can understand few of
> them. I think others are to do with new line or so.

You are doing really well, believe it or not. Currently our regression 
test isn't smart enough to compare newlines correctly from different
platforms. This causes different sets of tests to appear to fail, 
depending on what platform (and version of python) you are running 
things from.

> The first test is to do with Martel. which I have not install at
> present.
> test test_align failed -- Writing: 'Ooops, Clustalw parsing requires
> Martel, available from:', expected: 'testing reading and writing clustal
> format...\012CLUSTAL X '

You are right on with your assesment of this -- once you install
Martel this error should hopefully go away.

> test_gobase
> test test_gobase failed -- Writing: '\012', expected: '\015'
> test_prodoc
> test test_prodoc failed -- Writing: '\012', expected: '\015'
[...]
> test_rebase
> test test_rebase failed -- Writing: '\012', expected: '\015'
[...]

These tests failing are all due to line-break differences from Windows 
to UNIX machines. These tests were all written by Cayte, who works on
things from Windows, so right now the regression test can't compare
output from Windows with output generated by Linux because of the
different line feed conventions. So the code (and the testing code)
does work, it can just be a pain to deal with cross-platform line breaks.

If you run these failing tests singly (ie. 'python test_gobase.py',
etc.) then they should work properly (not generate any tracebacks). If 
this isn't the case feel free to ask again.
 
> I am using debian linux distro with python 2.0. I would appreciate, any
> help. If you need more information, please let me know.

Hope this helps. I'll add some info on this to the FAQ in the
tutorial. Don't hesitate to ask again if you have more questions.

Brad