--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/from_imgt.r	Fri Jul 24 04:44:39 2015 -0400
@@ -0,0 +1,56 @@
+library(data.table)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+infile="D:/wd/prisca/Mouse data Groningen July 2015/JIVFXVQ01_MAAIKE_1_PB_IGH_MID8_10nt_trimmed/1_Summary.txt"
+patient="JIVFXVQ01"
+sample="sample1"
+cell.count=10000
+receptor="IgH"
+output="D:/wd/prisca/mousetest.txt"
+
+infile=args[1]
+patient=args[2]
+sample=args[3]
+cell.count=args[4]
+receptor=args[5]
+output=args[6]
+
+dat = read.table(infile, header=T, sep="\t", fill=T, stringsAsFactors=F)
+dat = dat[,c("V.GENE.and.allele", "J.GENE.and.allele", "AA.JUNCTION", "Sequence")]
+
+dat = dat[dat$V.GENE.and.allele != "",]
+dat = dat[dat$J.GENE.and.allele != "",]
+dat = dat[dat$Sequence != "",]
+
+dat$V.GENE.and.allele = as.factor(as.character(lapply(strsplit(as.character(dat$V.GENE.and.allele), ", "), "[[", 1)))
+dat$J.GENE.and.allele = as.factor(as.character(lapply(strsplit(as.character(dat$J.GENE.and.allele), ", "), "[[", 1)))
+
+dat$V.GENE.and.allele = gsub("Homsap ", "", dat$V.GENE.and.allele)
+dat$V.GENE.and.allele = gsub("\\*.*", "", dat$V.GENE.and.allele)
+
+dat$J.GENE.and.allele = gsub("Homsap ", "", dat$J.GENE.and.allele)
+dat$J.GENE.and.allele = gsub("\\*.*", "", dat$J.GENE.and.allele)
+
+dat = data.frame(data.table(dat)[, list(Clone_Molecule_Count_From_Spikes=.N), by=c("V.GENE.and.allele", "J.GENE.and.allele", "AA.JUNCTION", "Sequence")])
+
+dat = dat[order(-dat$Clone_Molecule_Count_From_Spikes),]
+dat$perc = 100 / nrow(dat) * dat$Clone_Molecule_Count_From_Spikes
+
+dat$Log10_Frequency = log10(dat$perc / 100)
+
+dat$Patient = patient
+dat$Sample = sample
+dat$Receptor = receptor
+dat$Cell_Count = cell.count
+dat$Total_Read_Count = dat$Clone_Molecule_Count_From_Spikes
+dat$Related_to_leukemia_clone = F
+
+dat = dat[,c("Patient", "Receptor", "Sample", "Cell_Count", "Clone_Molecule_Count_From_Spikes", "Log10_Frequency", "Total_Read_Count", "V.GENE.and.allele", "J.GENE.and.allele", "Sequence" ,"AA.JUNCTION", "Related_to_leukemia_clone")]
+
+names(dat) = c("Patient", "Receptor", "Sample", "Cell_Count", "Clone_Molecule_Count_From_Spikes", "Log10_Frequency", "Total_Read_Count", "V_Segment_Major_Gene", "J_Segment_Major_Gene", "Clone_Sequence" ,"CDR3_Sense_Sequence", "Related_to_leukemia_clone")
+
+write.table(dat, output, quote=F, sep="\t", na="", dec=".", row.names=F, col.names=F)
+
+output
+