SH_samova.read

---  BASH interface of samova.R  ---

Usage example:
Rscript samova.R --test --drop_unclassified > samovar.log

Options:
--help: show this massage and exit
--test: use test data as input

-n:  number of data to generate. 1 by default
-o:  output csv file
-is: species name to initiate. character from table. most occured by default
-il: species level to initiate. mean of is amount by default
-k:  number of k-means to split the data. 10 by default
-mc: minimal amount of species per cluster. 2 by default

-trA:  treshhold to remove species amounts. 0 by default
-trP:  treshhold to remove species amounts. 2 by default
-nf: normalisation function of x. function(x) log10(x+1) by default
-pref: prefix of column names for new data
-inn: inner model for clusters. gaussian by default
-int: inter model for clusters. gaussian by default
--add:  add novel data to current table
--drop_unclassified: drop all unclassified and unknown levels
--calc_unclassified: calculate unclassified


To be implemented:
-r: runs as input
-d: desease as input
-t: csv data.frame as input
-nP: number of runs to process. only for -r and -d