--- a/igblast/igblast.r	Thu Aug 08 07:40:36 2019 -0400
+++ b/igblast/igblast.r	Thu Feb 25 13:36:15 2021 +0000
@@ -1,56 +1,56 @@
-args <- commandArgs(trailingOnly = TRUE)
-
-infile=args[1]
-outfile=args[2]
-
-blasted = read.table(infile, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="")
-
-blasted$ID = 1:nrow(blasted)
-blasted$VDJ.Frame = "Out-of-frame"
-
-search = blasted$inFrame == "true" & blasted$noStop == "false"
-if(sum(search) > 0){
-  blasted[search ,]$VDJ.Frame = "In-frame with stop codon"
-}
-
-search = blasted$inFrame == "true" & blasted$noStop == "true"
-if(sum(search) > 0){
-  blasted[search ,]$VDJ.Frame = "In-frame"
-}
-
-blasted$Top.V.Gene = blasted$vSegment
-blasted$Top.D.Gene = blasted$dSegment
-blasted$Top.J.Gene = blasted$jSegment
-blasted$CDR1.Seq = blasted$cdr1aa
-blasted$CDR1.Length = nchar(blasted$CDR1.Seq)
-blasted$CDR2.Seq = blasted$cdr2aa
-blasted$CDR2.Length = nchar(blasted$CDR2.Seq)
-blasted$CDR3.Seq = blasted$cdr3aa
-blasted$CDR3.Length = nchar(blasted$CDR3.Seq)
-blasted$CDR3.Seq.DNA = blasted$cdr3nt
-blasted$CDR3.Length.DNA = nchar(blasted$CDR3.Seq.DNA)
-blasted$Strand = "+/-"
-blasted$CDR3.Found.How = "found"
-
-search = blasted$cdr3nt == ""
-if(sum(search) > 0){
-  blasted[search,]$CDR3.Found.How = "NOT_FOUND"
-}
-
-blasted$AA.JUNCTION = blasted$CDR3.Seq
-
-n = c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "Functionality", "AA.JUNCTION")
-
-n[!(n %in% names(blasted))]
-
-blasted = blasted[,c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "AA.JUNCTION")]
-
-names(blasted) = c("frequency.count", "ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")
-
-#duplicate rows based on frequency.count
-blasted = blasted[rep(seq_len(nrow(blasted)), blasted$frequency.count),]
-blasted$ID = 1:nrow(blasted)
-
-blasted = blasted[,c("ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")]
-
-write.table(blasted, outfile, quote=F, sep="\t", row.names=F, col.names=T)
+args <- commandArgs(trailingOnly = TRUE)
+
+infile=args[1]
+outfile=args[2]
+
+blasted = read.table(infile, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="")
+
+blasted$ID = 1:nrow(blasted)
+blasted$VDJ.Frame = "Out-of-frame"
+
+search = blasted$inFrame == "true" & blasted$noStop == "false"
+if(sum(search) > 0){
+  blasted[search ,]$VDJ.Frame = "In-frame with stop codon"
+}
+
+search = blasted$inFrame == "true" & blasted$noStop == "true"
+if(sum(search) > 0){
+  blasted[search ,]$VDJ.Frame = "In-frame"
+}
+
+blasted$Top.V.Gene = blasted$vSegment
+blasted$Top.D.Gene = blasted$dSegment
+blasted$Top.J.Gene = blasted$jSegment
+blasted$CDR1.Seq = blasted$cdr1aa
+blasted$CDR1.Length = nchar(blasted$CDR1.Seq)
+blasted$CDR2.Seq = blasted$cdr2aa
+blasted$CDR2.Length = nchar(blasted$CDR2.Seq)
+blasted$CDR3.Seq = blasted$cdr3aa
+blasted$CDR3.Length = nchar(blasted$CDR3.Seq)
+blasted$CDR3.Seq.DNA = blasted$cdr3nt
+blasted$CDR3.Length.DNA = nchar(blasted$CDR3.Seq.DNA)
+blasted$Strand = "+/-"
+blasted$CDR3.Found.How = "found"
+
+search = blasted$cdr3nt == ""
+if(sum(search) > 0){
+  blasted[search,]$CDR3.Found.How = "NOT_FOUND"
+}
+
+blasted$AA.JUNCTION = blasted$CDR3.Seq
+
+n = c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "Functionality", "AA.JUNCTION")
+
+n[!(n %in% names(blasted))]
+
+blasted = blasted[,c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "AA.JUNCTION")]
+
+names(blasted) = c("frequency.count", "ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")
+
+#duplicate rows based on frequency.count
+blasted = blasted[rep(seq_len(nrow(blasted)), blasted$frequency.count),]
+blasted$ID = 1:nrow(blasted)
+
+blasted = blasted[,c("ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")]
+
+write.table(blasted, outfile, quote=F, sep="\t", row.names=F, col.names=T)