Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
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Begin refactoring of DensityData, refactor MSU HPCC submission scripts #126
I started on this branch awhile ago before our renewed effort to refactor some MergeData and DensityData.
This PR includes code that minimizes the amount of "helper" code in DensityData.
It also includes some needed changes in the MSU HPCC submission scripts and analysis of the examples in the paper (some of the code for the examples was really ugly and some users had difficulty building off of it. I will have to revisit the example analysis code once we finish all of our changes. Any big changes to DensityData will break that example code.
All of the tests work, but as previously mentioned, some of these changes may impact the way the example code is run. Despite that, I want to merge it in before we begin changing MergeData and DensityData due to the fact that I believe these changes will make it easier to refactor the two files later on. I attempted to move a significant chunk of the helper code out of DensityData into density_utils.py. That would make reconciling MergeData and DensityData easier. I imagine eventually this density_utils.py file will be removed, and some of the methods inside re-created or removed entirely.
Note, anything with a .sb file suffix is a file related to running commands/example code on the MSU HPCC.
teresi
commented
1 week ago
Hi Michael,
I started on this branch awhile ago before our renewed effort to refactor some
MergeDataandDensityData.This PR includes code that minimizes the amount of "helper" code in
DensityData. It also includes some needed changes in the MSU HPCC submission scripts and analysis of the examples in the paper (some of the code for the examples was really ugly and some users had difficulty building off of it. I will have to revisit the example analysis code once we finish all of our changes. Any big changes to DensityData will break that example code.All of the tests work, but as previously mentioned, some of these changes may impact the way the example code is run. Despite that, I want to merge it in before we begin changing
MergeDataandDensityDatadue to the fact that I believe these changes will make it easier to refactor the two files later on. I attempted to move a significant chunk of the helper code out ofDensityDataintodensity_utils.py. That would make reconciling MergeData and DensityData easier. I imagine eventually thisdensity_utils.pyfile will be removed, and some of the methods inside re-created or removed entirely.Note, anything with a
.sbfile suffix is a file related to running commands/example code on the MSU HPCC.