合并kraken的report文件，R

system("awk -F '\t' '{print $1}' *RNAreport|sort|uniq >uniq.names")
RNAsample<-c("127","22","129","81","138","99","140","20","132","82","149","73","120","105","148","44","122","101","124","100","143","76","133","12","145","79","152","77","118","102","147","80","121","106","151","104","135","38","136","2","150","78","146","55","141","11","137","97")

library(tidyverse)
read.table("uniq.names",header=F,sep="\t",quote="")->a

unique(a)->a
for (i in RNAsample){read.table(paste(i,".RNAreport",sep=""),header=F,sep="\t",quote="",fill=T)->b; colnames(b)[2]<-i;left_join(a,b,by="V1")->a;a[!duplicated(a[,1]),]->a;print(i);print(date())} #使用merge或者left_join功能时，注意每次循环后都要删除重复行，不然文件会越滚越大，运行越来越慢
a[is.na(a)]<-0
write.table(a,file="RNAabd.kraken",row.names=F,col.names=T,quote=F,sep=",")

 

system("awk -F '\t' '{print $1}' *DNAreport|sort|uniq >uniq.names")
DNAsample<-c("127","22","129","48","138","47","140","20","132","18","149","73","120","105","148","44","122","30","124","26","143","34","133","12","145","21","152","10","118","102","147","80","121","1","151","35","135","38","136","2","150","17","146","55","141","11","137","97")
 

library(tidyverse)
read.table("uniq.names",header=F,sep="\t",quote="")->a

unique(a)->a
for (i in DNAsample){read.table(paste(i,".DNAreport",sep=""),header=F,sep="\t",quote="",fill=T)->b; colnames(b)[2]<-i;left_join(a,b,by="V1")->a;a[!duplicated(a[,1]),]->a;print(i);print(date())}
a[is.na(a)]<-0
write.table(a,file="DNAabd.kraken",row.names=F,col.names=T,quote=F,sep=",")