[Biopython-dev] biopython-1.51 test log, sage inclusion

[Peter]

On Mon, Aug 17, 2009 at 10:31 PM, Marshall Hampton<mhampton at d.umn.edu> wrote:
>
> I hope this isn't too much email, I can just post to the dev list if
> you'd like.

Doing it on the mailing list is fine, I'd read it either way ;)

> Anyway, I manually ran my last test failure, test_SeqIO_online.py,
> and when I do that everything looks OK:
>
> thorn:16:28:30:site-packages: sage -python Tests/test_SeqIO_online.py
> Checking Bio.ExPASy.get_sprot_raw()
> - Fetching O23729
>  Got MAPAMEEIRQAQRAEGPAA...GAE [5Y08l+HJRDIlhLKzFEfkcKd1dkM] len 394
> Checking Bio.Entrez.efetch()
> - Fetching X52960 from genome as fasta
>  Got TGGCTCGAACTGACTAGAA...GCT [Ktxz0HgMlhQmrKTuZpOxPZJ6zGU] len 248
> - Fetching X52960 from genome as gb
>  Got TGGCTCGAACTGACTAGAA...GCT [Ktxz0HgMlhQmrKTuZpOxPZJ6zGU] len 248
> - Fetching 6273291 from nucleotide as fasta
>  Got TATACATTAAAGGAGGGGG...AGA [bLhlq4mEFJOoS9PieOx4nhGnjAQ] len 902
> - Fetching 6273291 from nucleotide as gb
>  Got TATACATTAAAGGAGGGGG...AGA [bLhlq4mEFJOoS9PieOx4nhGnjAQ] len 902
> - Fetching 16130152 from protein as fasta
>  Got MKVKVLSLLVPALLVAGAA...YQF [fCjcjMFeGIrilHAn6h+yju267lg] len 367
> - Fetching 16130152 from protein as gb
>  Got MKVKVLSLLVPALLVAGAA...YQF [fCjcjMFeGIrilHAn6h+yju267lg] len 367
>
> Not sure where to go from here, but it seems that things are basically
> working correctly.
>
> -Marshall Hampton

That fits with it being a transient network issue. Some of our
units tests like Tests/test_SeqIO_online.py are simple "print
and compare" scripts, which are intended to be run via the
run_tests.py script to validate their output. You can try this:
sage -python Tests/run_tests.py test_SeqIO_online.py

Or, manually compare that output to the expected output in
file Tests/ouput/test_SeqIO_online - but it looks fine to me
by eye.

Peter