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sjteresi / TE_Density

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
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Explain and differentiate process.py, preprocess.py, and density.py #57

Closed sjteresi closed 3 years ago

sjteresi commented 3 years ago

I am getting a little confused. I originally thought density.py was being refactored into process and preprocess. Removing the need for density.py But I now see a few #TODOs in process_genome.py to implement code in density.py. A lot of the code in that file is obsolete and potentially in need of removal.

Perhaps you can explain your intention for each file (we ought to update the file docstring at the top, they are outdated and there may be duplicate code)?

teresi commented 3 years ago

your original understanding is correct: density.py is getting removed there may be outdated comments that will get cleared up soon

process_genome.py is the entry point to get command line args and to run the system preprocess.py creates the GeneData and TransposonData files there should be other components to do the overlap, summation, and normalization