[Biopython-dev] Bio.motifs.parse fails on meme files with version 4.10

[Marco Galardini]

Thanks Peter,

I'll open an issue and post a couple of examples as soon as I can, thank 
you.

Marco

On 13/01/15 15:25, Peter Cock wrote:
> Thanks Marco,
>
> I'll let Michael answer on the best way to fix this, but if you
> have some small failing examples already which could be
> shared for use as Biopython test cases that would be great.
>
> Are you familiar with GitHub? We now use that for our issue
> tracker, and while it does not directly support attaching
> files to issues, you can post text files to GitHub as "gists":
>
> https://github.com/biopython/biopython/issues
> https://gist.github.com
>
> Thanks,
>
> Peter
>
> On Tue, Jan 13, 2015 at 2:53 PM, Marco Galardini <marco at ebi.ac.uk> wrote:
>> Hi biopythoneers,
>>
>> just noticed that the current meme version (4.10.0_2) introduced a change in
>> its output file that breaks the biopython parser.
>>
>> The error is:
>>>> >from Bio import motifs
>>>>> motifs.read(open('meme.txt'), 'meme')
>> Traceback (most recent call last):
>>    File "<stdin>", line 1, in <module>
>>    File "/usr/local/lib/python2.7/dist-packages/Bio/motifs/__init__.py", line
>> 141, in read
>>      motifs = parse(handle, format)
>>    File "/usr/local/lib/python2.7/dist-packages/Bio/motifs/__init__.py", line
>> 77, in parse
>>      record = meme.read(handle)
>>    File "/usr/local/lib/python2.7/dist-packages/Bio/motifs/meme.py", line 41,
>> in read
>>      length, num_occurrences, evalue = __read_motif_statistics(line)
>>    File "/usr/local/lib/python2.7/dist-packages/Bio/motifs/meme.py", line
>> 219, in __read_motif_statistics
>>      length = int(ls[3])
>> ValueError: invalid literal for int() with base 10: '='
>>
>> Relevant line before:
>> MOTIF  1        width =  19  sites =   3  llr = 43  E-value = 6.9e-002
>> Relevant line now:
>> MOTIF  1 MEME    width =  19  sites =   3  llr = 43  E-value = 6.9e-002
>>
>> A possible ugly workaround would be to change the way this line is parsed
>> (doing splits on 'width' and the other parameters). If you like I can try to
>> implement the fix myself and a couple of tests, just let me know.
>>
>> Marco
>>
>> --
>> Marco Galardini
>> Postdoctoral Fellow
>> EMBL-EBI - European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge CB10 1SD, UK
>> Phone: +44 (0)1223 49 2547
>>
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>> Biopython-dev mailing list
>> Biopython-dev at mailman.open-bio.org
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-- 
Marco Galardini
Postdoctoral Fellow
EMBL-EBI - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 49 2547