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

[Marshall Hampton]

I hope this isn't too much email, I can just post to the dev list if you'd 
like.  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

On Mon, 17 Aug 2009, Marshall Hampton wrote:

>
> On Mon, 17 Aug 2009, Peter wrote:
>> This one should be simple: test_EMBOSS.py
>> ValueError: Disagree on file ig IntelliGenetics/VIF_mase-pro.txt in
>> genbank format: 16 vs 1 records
>> This is a known regression in EMBOSS 6.1.0 which will be fixed
>> in their next release. Can you check this by running embossversion?
>
> My emboss version is 6.1.0, so that explains that.
>
> After copying the Tests folder from the source to my site-packages directory, 
> most of the errors go away, except for the one mentioned above and this one:
>
> ERROR: test_SeqIO_online
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "run_tests.py", line 248, in runTest
>    suite = unittest.TestLoader().loadTestsFromName(name)
>  File "/Users/mh/sagestuff/sage-4.1/local/lib/python/unittest.py", line 576, 
> in loadTestsFromName
>    module = __import__('.'.join(parts_copy))
>  File "test_SeqIO_online.py", line 62, in <module>
>    record = SeqIO.read(handle, format) # checks there is exactly one record
>  File 
> "/Users/mh/sagestuff/sage-4.1/local/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", 
> line 485, in read
>    raise ValueError("No records found in handle")
> ValueError: No records found in handle
>
> ...not sure what the problem might be with that.
>
> -Marshall
>