From 535fb42cd7d06d4393aa37ce0ce2de14da21dc6b Mon Sep 17 00:00:00 2001
From: Yuuki Galaxy <galaxy001@gmail.com>
Date: Wed, 21 Oct 2020 17:50:53 +0800
Subject: [PATCH] 	new file:   dodseq.r

---
 R/deseq2/dodseq.r | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100755 R/deseq2/dodseq.r

diff --git a/R/deseq2/dodseq.r b/R/deseq2/dodseq.r
new file mode 100755
index 000000000..6ea076045
--- /dev/null
+++ b/R/deseq2/dodseq.r
@@ -0,0 +1,32 @@
+#!/usr/bin/env littler
+
+if (length(argv)<2) {
+    cat("Usage ./dodseq.r <prefix.featureCounts.txt> <Nctl,Nexp> [prefix]\n")
+    quit()
+}
+inFile <- argv[1]
+ExpCnt <- as.numeric(unlist(strsplit(argv[2],',',fixed=T)))
+outP <- argv[3]
+if (length(argv)==2) {
+    outP <- unlist(strsplit(inFile,'.',fixed=T))[1]
+}
+cat(sep='',"[!]From [",inFile,"],Design [",ExpCnt[1],':',ExpCnt[2],"],Prefix [",outP,"].\n")
+
+countdata <- read.table(inFile, header=TRUE, row.names=1)
+countdata <- countdata[ ,6:ncol(countdata)]
+colnames(countdata) <- gsub("^alnSTAT\\.", "", colnames(countdata))
+colnames(countdata) <- gsub("Aligned\\.sortedByCoord\\.out\\.[sb]am$", "", colnames(countdata))
+countdata <- as.matrix(countdata)
+
+tFileDim <- dim(countdata)
+tExpSize <- ExpCnt[1]+ExpCnt[2]
+if ( tFileDim[2] != tExpSize ) {
+    cat("[x]Design size",tExpSize,"not matching with file column size",tFileDim[2],"!\n[!]File columns:[")
+    cat(sep=',',colnames(countdata))
+    cat("].\n")
+    quit()
+}
+
+print(head(countdata))
+cat(colnames(countdata),"\n")
+cat(dim(countdata),"\n")
-- 
2.11.4.GIT