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hmgu-itg / peakplotter

A tool to find and annotate signals in next-generation association studies
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Replace `plotpeaks.sh` with python scripts #2

Closed youngchanpark closed 3 years ago

youngchanpark commented 3 years ago

So plotpeaks.sh is quite a large script with a lot of functionality. I initially packaged peakplotter around this script because it would take a lot of time to disassemble plotpeaks.sh and transfer all it's functionality to python code.

We want to transfer to python because:

  1. Exit code other than 0 in bash does not stop the run
  2. Can't write tests for bash, but can with Python

For problem 1, I guess we could switch the plotpeaks.sh execution with bash strict mode for the time being, but this isn't really a solution. Just a workaround while we work on the transfer.

youngchanpark commented 3 years ago

We also need to preserve the functionality where plotpeaks.sh accepts comma-separated bfiles. This was implemented to allow peakplotter to run on meta-analysis association files.