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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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Functionality to customize overlap data output location #14

Closed sjteresi closed 4 years ago

sjteresi commented 4 years ago

Let me know what you think about it. I added a command line argument to the script. It defaults to \tmp and you can set a custom path with the -s flag. I wrote about it in the README too. The directory path is fed into OverlapData as an init argument.

teresi commented 4 years ago

yea, that's good

a small thing: I have noticed you are typically verbose: you have good descriptions and you can make them better by being more concise

e.g.

Functionality to customize overlap data output location

could be: add input arg for disk cache

Gene and TE overlap values are an intermediate calculation in this pipeline. However the overlap values can become quite large, so they must be stored in a temporary location. The script defaults to storing the compressed overlap files at /tmp however with the -s option the user can specify a different directory to output the overlap files.

could be: temporary cache directory, default /tmp and even better it could just be in the usage from ./density.py --help, so you don't have one documentation chasing another (e.g. DRY)