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

[Marshall Hampton]

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