[Biopython-dev] SearchIO.parse HMMER3 issue

[João Rodrigues]

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'
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>