--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline/filter.r	Fri Feb 19 15:10:54 2021 +0000
@@ -0,0 +1,55 @@
+arg = commandArgs(TRUE)
+summaryfile = arg[1]
+gappedfile = arg[2]
+selection = arg[3]
+output = arg[4]
+print(paste("selection = ", selection))
+
+
+summarydat = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote = "")
+gappeddat = read.table(gappedfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote = "")
+
+fix_column_names = function(df){
+    if("V.DOMAIN.Functionality" %in% names(df)){
+        names(df)[names(df) == "V.DOMAIN.Functionality"] = "Functionality"
+        print("found V.DOMAIN.Functionality, changed")
+    }
+    if("V.DOMAIN.Functionality.comment" %in% names(df)){
+        names(df)[names(df) == "V.DOMAIN.Functionality.comment"] = "Functionality.comment"
+        print("found V.DOMAIN.Functionality.comment, changed")
+    }
+    return(df)
+}
+
+gappeddat = fix_column_names(gappeddat)
+
+#dat = data.frame(merge(gappeddat, summarydat, by="Sequence.ID", all.x=T))
+
+dat = cbind(gappeddat, summarydat$AA.JUNCTION)
+
+colnames(dat)[length(dat)] = "AA.JUNCTION"
+
+dat$VGene = gsub("^Homsap ", "", dat$V.GENE.and.allele)
+dat$VGene = gsub("[*].*", "", dat$VGene)
+
+dat$DGene = gsub("^Homsap ", "", dat$D.GENE.and.allele)
+dat$DGene = gsub("[*].*", "", dat$DGene)
+
+dat$JGene = gsub("^Homsap ", "", dat$J.GENE.and.allele)
+dat$JGene = gsub("[*].*", "", dat$JGene)
+
+print(str(dat))
+
+dat$past = do.call(paste, c(dat[unlist(strsplit(selection, ","))], sep = ":"))
+
+dat = dat[!duplicated(dat$past), ]
+
+print(paste("Sequences remaining after duplicate filter:", nrow(dat)))
+
+dat = dat[dat$Functionality != "No results" & dat$Functionality != "unproductive",]
+
+print(paste("Sequences remaining after functionality filter:", nrow(dat)))
+
+print(paste("Sequences remaining:", nrow(dat)))
+
+write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T)