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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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HiCExplorer compatability with python 3.10? #811

Open torchij opened 2 years ago

torchij commented 2 years ago

It appears that the current HiCExplorer is not compatible with python 3.10. The issue looks to be related to the 'collections' module import syntax:

Traceback (most recent call last): File "/usr/local/bin/hicPlotMatrix", line 4, in <module> from hicexplorer.hicPlotMatrix import main File "/usr/local/lib/python3.10/dist-packages/hicexplorer/hicPlotMatrix.py", line 6, in <module> from hicmatrix import HiCMatrix File "/usr/local/lib/python3.10/dist-packages/hicmatrix/HiCMatrix.py", line 28, in <module> from intervaltree import IntervalTree, Interval File "/usr/local/lib/python3.10/dist-packages/intervaltree/__init__.py", line 22, in <module> from .intervaltree import IntervalTree File "/usr/local/lib/python3.10/dist-packages/intervaltree/intervaltree.py", line 37, in <module> class IntervalTree(collections.MutableSet): AttributeError: module 'collections' has no attribute 'MutableSet'

A similar issue was discussed here: https://www.elucidatedrones.com/posts/dronekit-python-error-in-python-3-10/

torchij commented 2 years ago

Original error was coming from out of date intervaltree module. A new error has surfaced with latest IntervalTree (v 3.1) and hiCExplorer (v3.7.2).

Traceback (most recent call last): File "/usr/local/bin/hicPlotMatrix", line 4, in <module> from hicexplorer.hicPlotMatrix import main File "/usr/local/lib/python3.10/dist-packages/hicexplorer/hicPlotMatrix.py", line 2, in <module> from collections.abc import OrderedDict ImportError: cannot import name 'OrderedDict' from 'collections.abc' (/usr/lib/python3.10/collections/abc.py)

Fix should be to update hicPlotMatrix.py to: from collections import OrderedDict

surabhiranavat commented 1 year ago

Hello,

I am getting the following error which looks similar to the one above: Traceback (most recent call last): File "/srv/home/sran0007/./HiCExplorer/bin/hicBuildMatrix", line 4, in <module> from hicexplorer.hicBuildMatrix import main File "/srv/home/sran0007/.local/lib/python3.10/site-packages/hicexplorer/hicBuildMatrix.py", line 24, in <module> from intervaltree import IntervalTree, Interval File "/srv/home/sran0007/.local/lib/python3.10/site-packages/intervaltree/__init__.py", line 22, in <module> from .intervaltree import IntervalTree File "/srv/home/sran0007/.local/lib/python3.10/site-packages/intervaltree/intervaltree.py", line 37, in <module> class IntervalTree(collections.MutableSet): AttributeError: module 'collections' has no attribute 'MutableSet'

This is when I'm trying to use hicBuildMatrix (with python 3.10.4, hicexplorer v2.2.1.1 even when I specify v3.7.2 with installation via conda). Could you please help diagnose this issue?

Thanks, Surabhi