I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.
Below is the code I am using

computeMatrix reference-point --referencePoint TSS \
-b 1000 -a 1000 \
-R ~/Desktop/ATAC/ATAC/Inducible_elements_Greenberg.bed \
-S ~/Desktop/ATAC/Control.mRp.clN.bigWig \
--skipZeros \
-o ~/Desktop/ATAC/matrix_controlmRPATACBasalcomputematrix.gz \

But I get the following error

File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'cfloat'?

These are the packages in my Conda environment

# packages in environment at /Users/abhinavsoni/anaconda3/envs/ATAC_Seq:
# Name                    Version                   Build  Channel
bzip2                     1.0.8                h3422bc3_4    conda-forge
ca-certificates           2023.5.7             hf0a4a13_0    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libcxx                    16.0.3               h4653b0c_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libsqlite                 3.41.2               hb31c410_1    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
llvm-openmp               16.0.3               h1c12783_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
numpy                     1.23.0          py310h0a343b5_0    conda-forge
openssl                   3.1.0                h53f4e23_3    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
python                    3.10.11         h3ba56d0_0_cpython    conda-forge
python_abi                3.10                    3_cp310    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge

What could be its possible work around?


1 Answer 1


It worked, I installed a the newer version of deeptools, from GitHub:



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