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MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Apache License 2.0
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pyBigWig values method does not take argument numpy=True #117

Closed tanjimin closed 1 week ago

tanjimin commented 1 year ago

https://github.com/MiraldiLab/maxATAC/blob/83cd5d2b95037cb2b100f72c0545e244336de72c/maxatac/utilities/normalization_tools.py#L47

  File "/gpfs/home/.conda/envs/maxatac/lib/python3.9/site-packages/maxatac/utilities/genome_tools.py", line 236, in chromosome_blacklist_mask
    return blacklist_bigwig_stream.values(chromosome,
TypeError: values() takes no keyword arguments

Same format in another file: https://github.com/MiraldiLab/maxATAC/blob/83cd5d2b95037cb2b100f72c0545e244336de72c/maxatac/utilities/genome_tools.py#L239

Removing numpy=True seems to resolve the issue.

tacazares commented 1 year ago

Hey @tanjimin, This is a known issue, https://github.com/MiraldiLab/maxATAC/issues/87 and https://github.com/MiraldiLab/maxATAC/issues/96#issuecomment-1130317957, that is due to the inability of pybigwig to recognize that your system has numpy installed. Try some of the suggested tips, I am not sure how removing the numpy=True fix will affect the import of values/downstream processes. Take care, Tareian