[Biopython-dev] SearchIO.parse HMMER3 issue

[Wibowo Arindrarto]

Hey Joao,

No problem. The discussion with the user went to private exchanges
anyway, so it was not indeed publicly searchable. In any case, I
posted this in our issue tracker (also to remind myself about this :)
): https://github.com/biopython/biopython/issues/313. If you find
anything else breaking or something you'd like to have, feel free to
post there directly.

Cheers,
Bow

On Fri, Apr 25, 2014 at 1:38 AM, João Rodrigues <anaryin at gmail.com> wrote:
> Hey Bow,
>
> Thanks, didn't know if it was known or not and I usually don't use these
> sequence parsers so.. :) Removing it did the trick indeed, seemed the most
> practical option.
>
> Cheers,
>
> João
>
>
> 2014-04-25 1:36 GMT+02:00 Wibowo Arindrarto <w.arindrarto at gmail.com>:
>
>> Hi Joao,
>>
>> Yes, this is a known issue with version 3.1b1. And indeed, the cause
>> is the '[ok]' line (just one last line in the file). I haven't
>> finished testing some cases (and I intended to add proper support for
>> 3.1 ~ a.ka. nhmmer + nhmmscan ~ with the update), so my updates for
>> this has not been up (probably sometime next week, not guaranteeing
>> anything though..). But if you need a quick solution, removing the
>> '[ok]' line fixes the problems in my case.
>>
>> Which reminds me, I think I need to properly track this issue in our
>> issue tracker :). There is an earlier post reporting this issue
>> (http://permalink.gmane.org/gmane.comp.python.bio.general/8027), but I
>> think we ended up emailing privately (where I mentioned this issue).
>>
>> Anyway, thanks for the report.
>>
>> Cheers,
>> Bow
>>
>> On Fri, Apr 25, 2014 at 1:27 AM, João Rodrigues <anaryin at gmail.com> wrote:
>> > Hi all,
>> >
>> > I downloaded HMMER3.1b today and tried to use the SearchIO module to
>> > parse
>> > the results. I ran into a weird error, something to do with a regex.
>> >
>> > The problem seems to be that after the '//' line, there is another line
>> > with '[ok]' that breaks the parser. I'm running HMMER with pretty much
>> > default options so I guess something might have changed in the latest
>> > version or something weird is happening here with mine?
>> >
>> > Cheers,
>> >
>> > João
>> >
>> > Traceback (most recent call last):
>> >   File "do_hmmer.py", line 99, in <module>
>> >     results = SearchIO.read(ali_fname, 'hmmer3-text')
>> >   File
>> >
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/SearchIO/__init__.py",
>> > line 363, in read
>> >     second = next(generator)
>> >   File
>> >
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/SearchIO/__init__.py",
>> > line 316, in parse
>> >     yield qresult
>> >   File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
>> >     self.gen.throw(type, value, traceback)
>> >   File
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/File.py",
>> > line 77, in as_handle
>> >     yield fp
>> >   File
>> >
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/SearchIO/__init__.py",
>> > line 315, in parse
>> >     for qresult in generator:
>> >   File
>> >
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py",
>> > line 47, in __iter__
>> >     for qresult in self._parse_qresult():
>> >   File
>> >
>> > "/home/software/python-libs/lib64/python2.6/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py",
>> > line 110, in _parse_qresult
>> >     qid = regx.group(1).strip()
>> > AttributeError: 'NoneType' object has no attribute 'group'
>> >
>> > _______________________________________________
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>> > Biopython-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>