[Biopython] Bio.motifs raising Exceptions using pypy

[Peter Cock]

On Thu, Jul 11, 2013 at 12:05 PM, Marco Galardini
<marco.galardini at unifi.it> wrote:
> Dear Biopython team,
>
> I am using the Bio.motifs package to perform a motif search inside DNA
> sequences; the motif is retrieved from a MEME file.
>
> When using python 2.7 the search works just fine (biopython 1.61), even
> though a bit slow; when using pypy (2.0.2, biopython 1.61+) to speed things
> up the same script raises an exception, complaining about the presence of
> "N" chars inside the sequence.
>
> Here's the traceback:
>
> Traceback (most recent call last):
>   File "app_main.py", line 72, in run_toplevel
>   File "test.py", line 20, in <module>
>     for position, score in pssm.search(s.seq, threshold=score_t):
>   File "/usr/local/lib/pypy2.7/dist-packages/Bio/motifs/matrix.py", line
> 354, in search
>     score = self.calculate(s)
>   File "/usr/local/lib/pypy2.7/dist-packages/Bio/motifs/matrix.py", line
> 331, in calculate
>     score += self[letter][position]
>   File "/usr/local/lib/pypy2.7/dist-packages/Bio/motifs/matrix.py", line
> 113, in __getitem__
>     return dict.__getitem__(self, letter)
> KeyError: 'N'
>
> If needed, I can provide you with the input files and a sample script.
>
> Thanks for the help, and keep up with the great work.
>
> Marco

A short test script (which we maybe can turn into another unit
test for this code) would be great to sort this out. Thanks!

Peter