scripts/old/misc/fix_bad_columns.R

In ahopki14/immunoSeqR: Tools for analyzing data from Adaptive's ImmunoSeq platform

all_files <- list.files(pattern='.tsv')
dir.create('mod')
for(a in all_files){
	ds <- read.csv(a,sep='\t')
	cols <- grep('nucleotide|aminoAcid|count|estimatedNumberGenomes',names(ds))
	ds <- ds[,cols]
	count <- grep('count',names(ds))
	if(length(count)!=1){stop('Loaded incorrect number of columns for count field')}
	if(names(ds)[count]!='count'){names(ds)[count] <- 'count'}
	write.table(ds,file=paste0('mod/',a),sep='\t',quote=FALSE,row.names=FALSE)
	rm(ds)
	gc()
}