Improved sge module and updated Blast module - Githubissues

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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Improved sge module and updated Blast module #120

Closed sdhutchins closed 6 years ago

sdhutchins commented 6 years ago

Features Added:

Added a function that will parse output of qstat.
Added ftp path to windowmasker files.
Added and tested function for downloading windowmaskerfiles
Added a timeout to the ftp login
Added long awaited wait function to SGEJob
Added _archive function for ncbiftpclient class to help when updating
Added standalone ncbi-download.py script that has argparse incorporated

Notable Changes:

Changed CompGenBLASTn to OrthoBlastN since it's designed for orthology inference
Changed name of organisms and taxonomy ids file
Updated template pbs file
Added templates folder to Manager/config path
Remodeled qstat. Parses job information. Returns jobs ids and status.

New Issues

Ceratotherium simum simum's taxonomy id was changed to 310713 and Odobenus rosmarus divergens's is still 9708.