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hmgu-itg / peakplotter

A tool to find and annotate signals in next-generation association studies
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Remove `pybedtools` dependency #8

Closed youngchanpark closed 3 years ago

youngchanpark commented 3 years ago

The old plotpeaks.sh script utilised bedtools to do some region merging.

I wanted to preserve the use of bedtools when translating the bash script to python code. So I wrote a bedtools_merge function in peakit.py. This utilise the pybedtools package. Although since bedtools merge function isn't really a complicated one, it'd be nice to just make our own implementation and remove the dependency.

Another reason to remove pybedtools dependency is because I think you can't install pybedtools if you don't have samtools installed on your machine (due to pybedtool's dependency to pysam, and how pysam requires the samtools library to compile). I need to double check this though.

youngchanpark commented 3 years ago

pysam not being able to compile just seems to be a Python version 3.8.2 problem. Python version 3.8.2 is shipped with Catalina, and updating it to the latest version of 3.8(.10) fixed the problem.

https://stackoverflow.com/questions/64111015/pip-install-psutil-is-throwing-error-unsupported-architecture-any-workarou/64216988#64216988