[Biopython-dev] biopython-1.51 test log, sage inclusion
Marshall Hampton
mhampton at d.umn.edu
Mon Aug 17 21:25:28 UTC 2009
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
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