[Biopython-dev] biopython-1.51 test log, sage inclusion
Marshall Hampton
mhampton at d.umn.edu
Mon Aug 17 21:31:43 UTC 2009
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
>
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