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## Julia Bischof
## 02-22-2016
readIMGT<-function(data,filterNoResults=TRUE){
if(substr(strsplit(data,split="/")[[1]][length(strsplit(data,split="/")[[1]])],1,2) %in% c("3_","6_")){
newcolnames<-gsub(" |-","_",strsplit(readLines(data)[1],split="\t")[[1]])
newcolnames<-gsub("'","",newcolnames)
if(length(strsplit(readLines(data)[2],split="\t")[[1]])==3){
temp<-lapply(readLines(data),function(x){strsplit(x,split="\t")[[1]]})
for(i in 1:length(temp)){
if(length(temp[[i]])==3){
temp[[i]]<-c(temp[[i]],rep(" ",(length(newcolnames)-3)))
}
}
tab<-t(data.frame(temp[2:length(temp)], stringsAsFactors = F))
rownames(tab)<-as.numeric(seq(1, (length(temp)-1), 1))
}else{
tab<-data.frame(matrix(NA, nrow=0,ncol=length(newcolnames)))
tab<-rbind(tab,read.table(data,fill=TRUE,header=F,skip=1,sep="\t",as.is=TRUE))
}
colnames(tab)<-newcolnames
}else{
tab<-read.table(data,fill=TRUE,header=TRUE,sep="\t",as.is=TRUE,check.names=F)
colnames(tab)<-gsub(" |-","_",gsub("'","",colnames(tab)))
}
tab<-tab[,-ncol(tab)]
if(filterNoResults==T){
out<-grep("No results",tab[,3])
if(length(out)>0){
tab<-tab[-out,]
cat("...", length(out), "sequences were excluded\n")
}else{
cat("... no sequences were excluded\n")
}
}
return(tab)
}
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