diff imgt_loader/imgt_loader.r @ 20:9185c3dfc679 draft

Uploaded

--- a/imgt_loader/imgt_loader.r	Thu Dec 22 03:43:02 2016 -0500
+++ b/imgt_loader/imgt_loader.r	Fri Jan 27 03:44:18 2017 -0500
@@ -1,11 +1,13 @@
 args <- commandArgs(trailingOnly = TRUE)
 
 summ.file = args[1]
-aa.file = args[2]
-junction.file = args[3]
-out.file = args[4]
+sequences.file = args[2]
+aa.file = args[3]
+junction.file = args[4]
+out.file = args[5]
 
 summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T)
+sequences = read.table(sequences.file, sep="\t", header=T, quote="", fill=T)
 aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T)
 junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T)
 
@@ -30,8 +32,8 @@
 out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"]
 out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"]
 
-out[,"CDR3.Seq.DNA"] = junction[,"JUNCTION"]
-out[,"CDR3.Length.DNA"] = nchar(as.character(junction[,"JUNCTION"]))
+out[,"CDR3.Seq.DNA"] = sequences[,"CDR3.IMGT"]
+out[,"CDR3.Length.DNA"] = nchar(as.character(sequences[,"CDR3.IMGT"]))
 out[,"Strand"] = summ[,"Orientation"]
 out[,"CDR3.Found.How"] = "a"