diff bin/remove.db.tables.r @ 0:3ca58369469c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/remove.db.tables.r	Wed Dec 06 19:01:53 2017 -0500
@@ -0,0 +1,46 @@
+#!/usr/bin/env Rscript
+# Remove the genome entries from two ngs.plot system files:
+# default.tbl and dbfile.tbl.
+
+args <- commandArgs(T)
+if(length(args)>1){
+	gname.to.rm <- args[1]
+	feature.to.rm <- args[2]
+}else{
+	gname.to.rm <- args[1]
+}
+
+# Save to text output.
+progpath <- Sys.getenv('NGSPLOT')
+if(progpath == "") {
+	stop("Set environment variable NGSPLOT before run the program. See README for details.\n")
+}
+default.file <- file.path(progpath, 'database', 'default.tbl')
+dbfile.file <- file.path(progpath, 'database', 'dbfile.tbl')
+default.tbl <- read.delim(default.file)
+dbfile.tbl <- read.delim(dbfile.file)
+
+if(exists("feature.to.rm")){
+	default.tbl <- subset(default.tbl, !(Genome==gname.to.rm & Region==feature.to.rm))
+	dbfile.tbl <- subset(dbfile.tbl, !(Genome==gname.to.rm & Region==feature.to.rm))
+}else{
+	default.tbl <- default.tbl[default.tbl$Genome != gname.to.rm, ]
+	dbfile.tbl <- dbfile.tbl[dbfile.tbl$Genome != gname.to.rm, ]	
+}
+
+
+write.table(default.tbl, file=default.file, row.names=F, sep="\t", quote=F)
+write.table(dbfile.tbl, file=dbfile.file, row.names=F, sep="\t", quote=F)
+
+
+# getScore <- function(i, db.fi, default.fi){
+#     score <- 3 - length(intersect(as.matrix(default.fi[db.fi[i, "tag"], ]), as.matrix(db.fi[i, ])))
+#     return(score)
+# }
+
+# for (i in (1:dim(db.fi)[1])){
+#     anno.db.tbl[i, "dbScore"] <- getScore(i, db.fi, default.fi)
+# }
+
+# anno.version="0.01"
+# save(anno.tbl, anno.db.tbl, anno.version, file="database.RData")