Re-address the current ways that the various Orthologs modules handle the data/databases.

datasnakes / OrthoEvolution

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

https://orthoevolution.readthedocs.io/en/master/

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Re-address the current ways that the various Orthologs modules handle the data/databases. #106

Open grabear opened 6 years ago

grabear commented 6 years ago

Problem:

When using CompGenObjects, the initial runtime for a full file can take up to 5 minutes.

Solution:

In order to speed this up, it would be good to add the entire csv file to a database as is. After CompGenObjects has created its pre/post blast dictionaries, it would be good to store these there too. The duplicates dictionary takes the longest amount of time.

grabear commented 5 years ago

We are already using sqlite databases.

[ ] Create more reasonable data/filenames in Manager/config/data/*
[ ] Refactor various classes to function more smoothly with/without these data
[ ] Implement #105