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Welcome to the post_fastGEAR wiki!

This script was written with help from Marttinen Pekka and provides a python implementation of the scripts found here https://mostowylab.com/2017/02/26/fastgear/.

post_fastGEAR.py -h

Make various plots from fastGEAR output

optional arguments:

-h, --help	show this help message and exit
-i I	FastGEAR folder. Should have folders with gene names only no suffix or prefix
-o O	Ouput name
-g G	Genes of interest GOI list. Can be comma separated after flag GOI1,GOI2,GOI3 or a file.txt with one GOI per line. GOIs need to be named exactly as per fastGEAR run
-b B	Sample of interest SOI list. Can be comma separated after flag SOI1,SOI2,SOI3 or a file.txt with one SOI per line. SOIs need to be named exactly as per fastGEAR run
-t T	Threads
-y Y	Minimum y value to display gene name is scatter plot
-x X	Minimum y value to display gene name is scatter plot
-s S	Make scatter plot of recent Vs ancestral recombinations
-z Z	Make heatmap of recombinations. Default True
-u U	Make recombinations per gene plot. Default True
-a A	Include ancestral recombination. Default True
-r R	Exclude genes that had no recombination. Default True
-p P	Tree file for sample order OR txt file of samples in order one per line must end in .txt or will parse as tree file.