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HTO Demultiplex issue #3

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evenlode10 opened this issue Feb 8, 2025 · 0 comments
Open

HTO Demultiplex issue #3

evenlode10 opened this issue Feb 8, 2025 · 0 comments

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@evenlode10
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Hi this is a nice tool and the examples are much appreciated, many thanks! I've been using it for some ASAP-Seq(ATAC and protein) data. I've got to the demultiplex stage after generating the feature count matrix for my HTO hashtags.

fba demultiplex \

-i matrix_featurecount_HTO.csv.gz \
--output_directory demultiplexed \
-dm 1 \
-v 

Gives me an error:

Traceback (most recent call last):
File "/home//.local/bin/fba", line 8, in
sys.exit(main())
File "/home/
/.local/lib/python3.8/site-packages/fba/main.py", line 144, in main
_ = m.demultiplex_feature_barcoding(
File "/home//.local/lib/python3.8/site-packages/fba/demultiplex.py", line 455, in demultiplex_feature_barcoding
cells_demultiplexed, m_identity = demultiplex_nb(
File "/home/
/.local/lib/python3.8/site-packages/fba/demultiplex.py", line 126, in demultiplex_nb
c = cluster_kmedoids(m,
File "/home//.local/lib/python3.8/site-packages/fba/demultiplex.py", line 64, in cluster_kmedoids
dtype=np.int),
File "/home/
/.local/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'int'.
np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
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

Tried the other demultiplex options in the vignettes, similar issues.

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