flu-crew / octoFLU

Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
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Created python port of pipeline.sh v0.2 #11

Closed mazeller closed 5 years ago

mazeller commented 5 years ago

Missing MP check for FastTree Does not print all tree file names Does not do file exist check before checking NN in tree files Inconsistent subprocess calls -Not following any standard or protocol on which function or how it is run -shell = True is used for Windows use, but decreases performance on all platforms

Would recommend using the shell script on Mac/Linux systems, but the python file should replicate functionality in Windows/Mac environments.