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

[Peter Cock]

Thanks: https://github.com/biopython/biopython/issues/461

Peter

On Tue, Jan 13, 2015 at 3:29 PM, Marco Galardini <marco at ebi.ac.uk> wrote:
> 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
>>>
>>> _______________________________________________
>>> Biopython-dev mailing list
>>> Biopython-dev at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
>
>
> --
> 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
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