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pfenninglab / halLiftover-postprocessing

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Optional Histogram Argument #4

Closed EthanHolleman closed 3 years ago

EthanHolleman commented 3 years ago

Hello, thank you for all the work on this project! I am currently using HALPER on a server that was not making it easy for me to install matplotlib. I noticed that it seems this dependency is only required for creating the histograms at the end of the orthologFind.py script.

It was faster for me to conditionally import matplotlib than figure out what the issue was with pip on the server so I thought I'd share the code I added. Maybe it would be helpful for someone in a similar situation. Although it does seem the chances you are able to get numpy running and not matplotlib like in my case are low.

Main changes are to add a command line argument -noHist that is True by default and moving the matplotlib import statement into the make_hist function. If -noHist flag is passed then make_hist is never called.

badoi commented 3 years ago

Thanks Ethan! I also don't always use the matplotlib functions either. Just check that your alignments are meaningful w/out the QC plots.