Rscript_trees_retain_taxa.txt

# Rscript_trees_retain_taxa.txt

# usage:
# Rscript Rscript_trees_retain_taxa.txt intrees_file outtrees_file comma-separated,list,of,taxa,to,keep

library(ape)

args = commandArgs(trailingOnly=TRUE)
fileName = args[1] ## "RADtag_trees_phylogeny_major_groups.txt"
outfilename = args[2] ##"RADtag_trees_phylogeny_major_groups.collapsed_polytomies.txt"
good_taxa = read.csv(text = args[3], sep = ",", header = FALSE,stringsAsFactors = FALSE)
good_taxa = as.character(good_taxa[1,])
print(good_taxa )

conn <- file(fileName,open="r")
linn <-readLines(conn)
for (i in 1:length(linn)){
	print(i)
	intree = read.tree(text = linn[i])
	
	to_keep = intersect(intree$tip,good_taxa) # this can be of length <4; so need to discard entirely
	if (length(to_keep) >= 4) {
		to_drop = setdiff(intree$tip, to_keep)
	
		cleaned_tree = drop.tip(intree, to_drop, trim.internal = TRUE, subtree = FALSE, rooted = is.rooted(intree))
	
		write.tree(cleaned_tree, file = outfilename, append = TRUE,
			   digits = 10, tree.names = FALSE)
		}

}
close(conn)

# read-write again to cear issues!?
indat = read.tree(file = fileName)
write.tree(indat, file = fileName)