# HG changeset patch
# User morinlab
# Date 1480894163 18000
# Node ID 185b0aba7d8e6ec274687ec6b1fb92fc6c8e2a4f
# Parent  a39905a6413e45a12b64727547b954594cf69638
Uploaded

diff -r a39905a6413e -r 185b0aba7d8e merge.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.R	Sun Dec 04 18:29:23 2016 -0500
@@ -0,0 +1,35 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+files <- read.table(args[1], stringsAsFactors=F)
+
+my.read.table <- function(file) {
+    read.table(
+        file,
+        sep="\t",
+        stringsAsFactors=T,
+        header=as.logical(args[4])
+        )
+    }
+
+data <- NA;
+if (length(files) == 1) {
+    data <- my.read.table(files[1])
+    }
+else {
+    data_list <- apply(files, 1, my.read.table)
+    data <- Reduce(function(x,y) { rbind(x,y) }, data_list)
+    }
+
+contig_order <- read.table(args[2], stringsAsFactors=F)[,1]
+data[,1] <- factor(data[,1], levels=contig_order)
+data <- data[order(data[,1]),]
+data[,1] <- as.character(data[,1])
+
+write.table(
+    x=data,
+    file=args[3],
+    sep ="\t",
+    quote=F,
+    row.names=F,
+    col.names=as.logical(args[4])
+    )