magnitov / pentad Goto Github PK

Hello,
I'm having an issue when trying to run a get_pentad_cis.py script.
It recognizes my .cool file, but not the bedgraph file with the first eigenvector (PCA1) of a Hi-C matrix.
Whereas it says "You could use the ‘::’ syntax to specify a column name from the bedGraph file", there are no headers in my file and it looks like this:
chr1 0 2000000 0.009910410970
chr1 2000000 4000000 -0.034634710334
chr1 4000000 6000000 -0.042192360907
...
How can I specify that column? Or could there be an issue with the titles where it should explicitly end with bedGraph (capital "G") and not bedgraph?
Many thanks.

Hi Mikhail,
Could we extract centromere or telomere clusters and calculate their compartment strength using panted?
Best,
Pengfei

get_pentads_trans.py is based on cooltools(v0.3.2). However, environment.yml does not specify the version of cooltools so it will create an environment with the latest version of cooltools by default. Anyone who tries to run get_pentads_trans.py needs to uninstall cooltools first and reinstall cooltools(v0.3.2) with command "conda install -c bioconda cooltools=0.3.2"

Hello, I am having trouble installing pentads. I followed the install instructions, but when building the conda environment I get a series of errors. The first one appears to be:

Failed to build cooltools cytoolz pypairix

Which then cause a downstream series of errors. I'm wondering if you have any advice to solve this issue? I've included the entire error below.
Best,
Randi

Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/isenhart/opt/anaconda3/envs/pentads/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt']
Pip subprocess output:
Collecting cooler>=0.8.5
Using cached cooler-0.8.11-py2.py3-none-any.whl (100 kB)
Collecting cooltools>=0.5.0
Using cached cooltools-0.5.1.tar.gz (8.0 MB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting multiprocess
Using cached multiprocess-0.70.13-py37-none-any.whl (115 kB)
Requirement already satisfied: pandas in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.3.5)
Collecting h5py>=2.5
Using cached h5py-3.7.0-cp37-cp37m-macosx_10_9_x86_64.whl (3.1 MB)
Collecting click>=7
Using cached click-8.1.3-py3-none-any.whl (96 kB)
Collecting cytoolz<0.11
Using cached cytoolz-0.10.1.tar.gz (475 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: scipy>=0.16 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.7.3)
Collecting pyfaidx
Using cached pyfaidx-0.7.1-py3-none-any.whl
Collecting asciitree
Using cached asciitree-0.3.3-py3-none-any.whl
Collecting pyyaml
Using cached PyYAML-6.0-cp37-cp37m-macosx_10_9_x86_64.whl (189 kB)
Collecting simplejson
Using cached simplejson-3.17.6-cp37-cp37m-macosx_10_9_x86_64.whl (74 kB)
Collecting pypairix
Using cached pypairix-0.3.7.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: six in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: numpy>=1.9 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.21.6)
Collecting bioframe>=0.3.3
Using cached bioframe-0.3.3-py2.py3-none-any.whl (112 kB)
Requirement already satisfied: cython in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (0.29.32)
Collecting joblib
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Requirement already satisfied: matplotlib in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (3.5.3)
Collecting numba
Using cached numba-0.56.2-cp37-cp37m-macosx_10_14_x86_64.whl (2.4 MB)
Collecting scikit-learn
Using cached scikit_learn-1.0.2-cp37-cp37m-macosx_10_13_x86_64.whl (7.8 MB)
Collecting scikit-image
Using cached scikit_image-0.19.3-cp37-cp37m-macosx_10_13_x86_64.whl (13.2 MB)
Collecting requests
Using cached requests-2.28.1-py3-none-any.whl (62 kB)
Collecting importlib-metadata
Using cached importlib_metadata-4.12.0-py3-none-any.whl (21 kB)
Collecting toolz>=0.8.0
Using cached toolz-0.12.0-py3-none-any.whl (55 kB)
Requirement already satisfied: python-dateutil>=2.7.3 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from pandas->cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from pandas->cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (2022.2.1)
Requirement already satisfied: packaging>=20.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (21.3)
Requirement already satisfied: cycler>=0.10 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (4.37.3)
Requirement already satisfied: pyparsing>=2.2.1 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (3.0.9)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (1.4.4)
Requirement already satisfied: pillow>=6.2.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (9.2.0)
Collecting dill>=0.3.5.1
Using cached dill-0.3.5.1-py2.py3-none-any.whl (95 kB)
Collecting llvmlite<0.40,>=0.39.0dev0
Using cached llvmlite-0.39.1-cp37-cp37m-macosx_10_9_x86_64.whl (25.5 MB)
Requirement already satisfied: setuptools<60 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from numba->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (59.8.0)
Collecting networkx>=2.2
Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting imageio>=2.4.1
Using cached imageio-2.22.0-py3-none-any.whl (3.4 MB)
Collecting tifffile>=2019.7.26
Using cached tifffile-2021.11.2-py3-none-any.whl (178 kB)
Collecting PyWavelets>=1.1.1
Using cached PyWavelets-1.3.0-cp37-cp37m-macosx_10_13_x86_64.whl (4.3 MB)
Collecting threadpoolctl>=2.0.0
Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Requirement already satisfied: typing-extensions in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (4.3.0)
Collecting zipp>=0.5
Using cached zipp-3.8.1-py3-none-any.whl (5.6 kB)
Requirement already satisfied: certifi>=2017.4.17 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from requests->bioframe>=0.3.3->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (2022.9.14)
Collecting urllib3<1.27,>=1.21.1
Using cached urllib3-1.26.12-py2.py3-none-any.whl (140 kB)
Collecting charset-normalizer<3,>=2
Using cached charset_normalizer-2.1.1-py3-none-any.whl (39 kB)
Collecting idna<4,>=2.5
Using cached idna-3.4-py3-none-any.whl (61 kB)
Building wheels for collected packages: cooltools, cytoolz, pypairix
Building wheel for cooltools (setup.py): started
Building wheel for cooltools (setup.py): finished with status 'error'
Running setup.py clean for cooltools
Building wheel for cytoolz (setup.py): started
Building wheel for cytoolz (setup.py): finished with status 'error'
Running setup.py clean for cytoolz
Building wheel for pypairix (setup.py): started
Building wheel for pypairix (setup.py): finished with status 'error'
Running setup.py clean for pypairix
Failed to build cooltools cytoolz pypairix
Installing collected packages: pypairix, asciitree, zipp, urllib3, toolz, tifffile, threadpoolctl, simplejson, pyyaml, PyWavelets, pyfaidx, networkx, llvmlite, joblib, imageio, idna, h5py, dill, charset-normalizer, scikit-learn, scikit-image, requests, multiprocess, importlib-metadata, cytoolz, numba, click, bioframe, cooler, cooltools
Running setup.py install for pypairix: started
Running setup.py install for pypairix: finished with status 'error'

Pip subprocess error:
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [59 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/cooltools
copying cooltools/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools
copying cooltools/main.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/saddle.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/eigs_cis.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/util.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/eigs_trans.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/dots.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/insulation.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/pileup.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/expected_cis.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/sample.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/logbin_expected.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/expected_trans.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/genome.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/expected_smoothing.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/cool2cworld.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/pairs_scaling_functions.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/balance.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/contrast.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/peaks.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/checks.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/numutils.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/plotting.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/_query.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/io.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/schemas.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/common.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/runlength.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/saddle.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/directionality.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/coverage.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/insulation.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/expected.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/sample.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/eigdecomp.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/dotfinder.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/snipping.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
running build_ext
building 'cooltools.lib._numutils' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/cooltools
creating build/temp.macosx-10.9-x86_64-3.7/cooltools/lib
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/numpy/core/include -I/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/numpy/core/include -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c cooltools/lib/_numutils.c -o build/temp.macosx-10.9-x86_64-3.7/cooltools/lib/_numutils.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cooltools
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
[1/5] Cythonizing cytoolz/utils.pyx
[2/5] Cythonizing cytoolz/dicttoolz.pyx
[3/5] Cythonizing cytoolz/functoolz.pyx
[4/5] Cythonizing cytoolz/itertoolz.pyx
[5/5] Cythonizing cytoolz/recipes.pyx
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/compatibility.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/_version.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/init.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/_signatures.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/operator.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/init.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/exceptions.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/itertoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/dicttoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/functoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/recipes.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/init.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/recipes.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/functoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/dicttoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/cpython.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/itertoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_none_safe.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_utils.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_curried.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_compatibility.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_embedded_sigs.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_functoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_inspect_args.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_doctests.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_tlz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_signatures.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/dev_skip_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_recipes.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_docstrings.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_dev_skip_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_dicttoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_serialization.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_curried_toolzlike.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_itertoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
running build_ext
building 'cytoolz.dicttoolz' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/cytoolz
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c cytoolz/dicttoolz.c -o build/temp.macosx-10.9-x86_64-3.7/cytoolz/dicttoolz.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cytoolz
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
% (opt, underscore_opt)
running bdist_wheel
running build
running build_ext
building 'pypairix' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c src/bgzf.c -o build/temp.macosx-10.9-x86_64-3.7/src/bgzf.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pypairix
error: subprocess-exited-with-error

× Running setup.py install for pypairix did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
% (opt, underscore_opt)
running install
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
running build
running build_ext
building 'pypairix' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c src/bgzf.c -o build/temp.macosx-10.9-x86_64-3.7/src/bgzf.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pypairix

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

failed

CondaEnvException: Pip failed

Hi,
I was following the 'paper_code/02_technical_tests.sh' instruction to calculate compartments size, and then I want to calculate each compartments strength, I just don't understand what the 'hg19.100kb.windows.bed' file looks like, is it the chromosome size file?
Best,
Pengfei

Hello! Could you please tell me whether there is a possibility to calculate average compartment and visualize it in log2-scale?

Would be nice to add a few lines that check that chromosomes names in COOLER are the same as in BED (for instance, have or haven't "chr" part). Then try to correct chromosomes names in BED to match those in COOLER, and terminate the script failing to do so.

@Phocavitulina, can you implement this?

Hello developer:

Sorry to disturb you & thank you for this amazing tool.

Now I have question about how to define short- and long-range interactions? Because I'm work on plant not animal and probably I need use different parameters for analysis Hi‑C data.

Best,
Han

Hello! Thank you for your tool. I have a single question: when I'm running quant_strength_trans.py script I get a tsv file with strength of compartments A and B separately. I wonder whether it's possible to calculate compartment strength between A and B compartments?

Thanks in advance!