py3: relative imports fail

[endrebak]

(Conda gives a conflicting requirements error, so I installed metaseq with pip.)

When trying to import metaseq, I get the following error:

In [2]: import metaseq
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-3365faa9d779> in <module>()
----> 1 import metaseq

/local/home/endrebak/anaconda3/lib/python3.5/site-packages/metaseq/__init__.py in <module>()
      2 import sys
      3 import time
----> 4 import helpers
      5 from helpers import data_dir, example_filename
      6 from _genomic_signal import genomic_signal

ImportError: No module named 'helpers'

[endrebak]

If I am reading your Travis build log correctly, you only test on py27. Is this a requirement? If so, I guess I cannot use metaseq with snakemake as easily as I hoped. And you should add the requirement to your docs/README.md.

Pretend edit: tested conda install metaseq-all on py27 and it imports just fine.

[endrebak]

Relative imports were removed in py3 (good choice, imo), and this is why it fails. I fixed your metaseq/__init__.py like so:

import os
import sys
import time
from metaseq import helpers
from metaseq.helpers import data_dir, example_filename
from metaseq._genomic_signal import genomic_signal
import metaseq.plotutils
import integration
import integration.chipseq
import metaseq.colormap_adjust
import metaseq.results_table
import metaseq.tableprinter
from metaseq.version import __version__
import metaseq.persistence

but then I got this error:

In [1]: import metaseq
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-3365faa9d779> in <module>()
----> 1 import metaseq

/local/home/endrebak/anaconda3/lib/python3.5/site-packages/metaseq-0.5.6-py3.5.egg/metaseq/__init__.py in <module>()
      4 from metaseq import helpers
      5 from metaseq.helpers import data_dir, example_filename
----> 6 from metaseq._genomic_signal import genomic_signal
      7 import metaseq.plotutils
      8 import integration

/local/home/endrebak/anaconda3/lib/python3.5/site-packages/metaseq-0.5.6-py3.5.egg/metaseq/_genomic_signal.py in <module>()
     30
     31 import numpy as np
---> 32 from bx.bbi.bigwig_file import BigWigFile
     33
     34 import pybedtools

bx/bbi/bigwig_file.pyx in init bx.bbi.bigwig_file (lib/bx/bbi/bigwig_file.c:7691)()

bx/bbi/bbi_file.pyx in init bx.bbi.bbi_file (lib/bx/bbi/bbi_file.c:12911)()

ImportError: No module named 'cStringIO'

which I do not have time to look up now, but I'd guess it has to do with the same import issue.

[daler]

Yep, due to the dependency on bx-python, which itself is only py27, I can't make metaseq py3-compatible.

Whenever I need to use it within snakemake, I end up writing a separate script and run it in a py27 env. Awkward? Yes.

I think the best solution here is to replace bx-python with the py3-compatible pybigwig. That will require a bit of work and lots more tests. It's already on my list though.

That said, depending on what you need to do, deepTools might be a better option than metaseq.

[endrebak]

bx-python has actually been python3 compatible for a year or so, IIRC. Perhaps you should try installing it again?

But do not put this high on your todo-list for my sake, I'll easily find a workaround.

[daler]

The error you reported is a common error in non-py3-compatible code and, judging from your paths, is coming from bx-python as installed under py35. I had also tried building it a few months ago for py3 in bioconda and didn't have any luck. Are you able to use the bx.bbi.bigwig_file module in py3?

[endrebak]

Sorry, probably not! I always think bx = intervaltree, clustertree because it is the only two modules I use.

On Tue, May 24, 2016 at 3:46 PM, Ryan Dale [email protected] wrote:

The error you reported is a common error in non-py3-compatible code and, judging from your paths, is coming from bx-python as installed under py35. I had also tried building it a few months ago for py3 in bioconda and didn't have any luck. Are you able to use the bx.bbi.bigwig_file module in py3?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/daler/metaseq/issues/26#issuecomment-221274417

[endrebak]

When I learn more about bigwig, I'll try out https://bitbucket.org/mruffalo/bx-python3 and see if it works.

Perhaps it can be bundled with metaseq? It probably will not get more updates, but might be good enough.

[superbobry]

I think it might be more beneficial to port the original bx-python (which I believe is bxlab/bx-python) to Python3 rather than switching to an unmaintained fork.

@endrebak you could get Python3 behaviour in Python2 by importing

from __future__ import absolute_import

After this import the following

import metaseq.colormap_adjust
import metaseq.results_table
import metaseq.tableprinter

could be concisely written as

from . import colormap_adjust, results_table, tableprinter