--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_extract.sh	Thu Oct 22 09:18:30 2015 -0400
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+inputfile=$1
+outputfile=$2
+removeheader=$3	
+columns="$@"
+
+cols="${columns// /,}" #make comma-separated
+
+#skip first three arguments
+firstcomma=`expr index "$cols" ,`
+cols="${cols:$firstcomma}"
+secondcomma=`expr index "$cols" ,`
+cols="${cols:$secondcomma}"
+thirdcomma=`expr index "$cols" ,`
+cols="${cols:$thirdcomma}"
+cols="${cols//:/}" #remove colons
+echo "colums to print: $cols"
+
+arr=$(echo $cols | tr "," "\n")
+
+for x in $arr
+do
+    echo $x
+done
+
+myArray=($columns)
+i=3
+len=${#myArray[@]}
+mycols=""
+echo "len: $len"
+while [ $i -le $len ]
+do	
+	echo "myarray: ${myArray[$i]}"
+	mycols+=${myArray[$i]}
+	i=$[$i+2]
+done
+mycols="${mycols//:/,}" #make comma-separated
+mycols="${mycols%?}"
+echo "mycols: $mycols"
+
+awk 'BEGIN{
+		FS="\t";
+		OFS="\t";
+		columns="'"$mycols"'";
+		len=split(columns,arr,",")
+	}{
+	 if (index($1,"#")==1 || $1==""){ #print header as--s
+		if("'"$removeheader"'"=="N"){
+            print $0
+		}
+	 }	
+	 else{	
+		 for (i=1;i<len;i++){
+			j=arr[i]
+			printf $j"\t"
+		 }
+		 j=arr[len]
+		 printf $j"\n"	
+	}
+	}END{
+
+	}' $inputfile > $outputfile
+
+