[Biopython] test_Emboss.py, was: Biopython 1.6.0

[Peter Cock]

On Tue, Jun 26, 2012 at 1:11 PM, David Lapointe
<david.lapointe at gmail.com> wrote:
> Ubuntu 10.04
> Python 2.6.5
> Emboss 6.3.1
>
> These are the tests that fail, always. It may be because I have a
> wrapper around the application ( setting up the EMBOSS_VARS)
>
> ======================================================================
> FAIL: needle with the asis trick, output to a file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "test_Emboss.py", line 538, in test_needle_file
>    self.assertTrue(os.path.isfile(filename))
> AssertionError
>
> ======================================================================
> FAIL: water with the asis trick, output to a file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "test_Emboss.py", line 479, in test_water_file
>    self.run_water(cline)
>  File "test_Emboss.py", line 462, in run_water
>    self.assertTrue(os.path.isfile(cline.outfile))
> AssertionError
>
>
> On Tuesday, June 26, 2012, Peter wrote:
>
>   On Monday, June 25, 2012, Lapointe, David wrote:
>
>       Great!
>
>       I have EMBOSS installed but the tests always  fail the EMBOSS
> tests. They are on the $PATH.
>
>       David
>

Thanks David,

I've made a small change to give a more informative error in future:
https://github.com/biopython/biopython/commit/1d1f2a45658f808e22b8d0dbdcf2e6f825581fd7

However, I think problem is probably your wrapper script fails to
escape filenames with spaces. Both those failing tests use output
files with a space in their name. This might be useful to you:
http://www.biostars.org/post/show/18642/bash-dollar-at-variable-loses-quote-characters/

Regards,

Peter