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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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Completion of working DatabaseManagement. #145

Closed grabear closed 5 years ago

grabear commented 5 years ago
## Fixes issue - Fixed/tested `DatabaseManagement` and `DatabaseDispatcher` in with _db_mana_test.py_ - refseq_release now works (but only for systems with PBS jobs). - Added FTP error handling - Added progress bars when downloading or extracting files - Renamed `BioSQL` module to `biosql` to fix import issues with _biopython's_ `BioSQL` module - Added a means to use a dictionary to configure an SGE job ### Changes proposed in this pull request: - Added `Oven._check_ingredients()` to check for existing cookicutter directories - Moved many utility functions and classes to top level utilities.py - `FullUtilities`, `BlastUtils`, `ManagerUtils`, `CookieUtils`, `GenbankUtils`, etc. - Added `system_cmd` wrapper for Popen, which also streams the _stderr/stdout_ - Standardized config files located in the package for _database management_ - Archived the `streamio` module - Archived random `BlastUtils`