--- a/rmsk_summary_table_multiple.r	Fri Feb 07 02:25:47 2020 -0500
+++ b/rmsk_summary_table_multiple.r	Fri Feb 07 06:06:47 2020 -0500
@@ -3,19 +3,12 @@
 # analysis of *.out file
 # input arguments: <rmsk_result.out> <reads.fas.
 # calculates totoal proportion of matched repetetive families and averagee score and print the table 
-suppressPackageStartupMessages(library(getopt))
 
-# INPUT ARGUMENTS:
-opt = getopt(matrix(c(
-  'fasta', 'f', 1, "character",		
-  'repeat_masker','r', 1, "character",
-  'output', 'o', 1, "character",
-  'help','h',0,'logical'),ncol=4,byrow=T))
+opt = list()
+opt$fasta = commandArgs(T)[1]
+opt$repeat_masker = commandArgs(T)[2]
+opt$output = commandArgs(T)[3]
 
-if (!is.null(opt$help)) {
-cat("Usage:\n\n -f   fasta file \n -r   repeat masker output\n -o   output files\n")
-stop()
-}
 
 RMfiles=system(paste("ls ",opt$repeat_masker,sep=""),intern=T)
 fasta=system(paste("ls ",opt$fasta,sep=""),intern=T)
@@ -23,8 +16,8 @@
 
 
 getsubdir=function(x){
-	xx=gsub(".*/","",x)	
-	sdir=gsub(xx,"",x,fixed=T)
+	xx=gsub(".*/","",x)
+  sdir=gsub(xx,"",x,fixed=T)
 	sdir
 }