Closed tiagoantao closed 10 years ago
A more general comment: I pip3 installed bcbio-gff, but the existing version is not 3 compatible at all. I can work on this, if there is interest. I am half-way through it in any case.
I think I have found the cause: the version for python 3 on pypi seems so be 2.0. The version on github works fine. But the version on pypi is not 2to3... Should be trivial to sort out, thus...
Tiago; Apologies, I haven't done any work to make this Python 3 compatible beyond what @khughitt contributed in #78. More generally, I'm hoping to contribute the Biopython parts of this to Ryan's GFFutils library to: https://github.com/daler/gffutils
I'm definitely happy to accept patches if you think it's worth making this more Python 3 compatible before the merge happens.
I ended up implementing a simple parser myself. I think that the problem is that the pypi upload for some reason reverts to version 2 formatting (no 2to3 usage). This means that it installs, on python 3, python 2 code.
If one git clones then everything seemed to work perfectly (2to3 is run, all seemed to work correctly)
@chapmanb @tiagoantao It looks the version on PyPi has not been updated yet to include the above-mentioned Python 3 patch. Once that is pushed, then it should work with a normal pip install
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Keith, Tiago; Argh, I suck. Sorry I thought I'd pushed an updated version and hadn't tested since I'm not yet using Python 3. I pushed a new 0.4 version which should have all of the Keith's fixes, so hopefully it'll work cleanly now. Sorry about the issues and confusion.
@chapmanb It happens :)
The current GFF code does not work with Python 3. gff/BCBio/GFF/init.py needs local referencing with P3: from .GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple from .GFFOutput import GFF3Writer, write
(note the . before GFFParser and GFFOutput)