Hi dear Biostars community,
I am trying to find a quick and easy way to square root transform my the read counts of my biom OTU table using the PhyloToAST program. After installing the program and all dependencies, I run the following command in my terminal: phylotoast.biom_calc.transform_raw_abundance(otu_table.biom, fn=math.log10, sampleIDs=True, sample_abd=True) and get the following error -bash: syntax error near unexpected token `otu_table.biom,'
Surely I'm doing something wrong and probably very obvious but unfortunately I can't find the solution as there is little information on how to use the script (http://phylotoast.readthedocs.io/en/latest/scripts/biom_calc.html).
Help on this issue would be greatly appreciated. Thanks!