fastq_fullnames=function(fastq_path){
#get the fullnames of fastq files
fn2=list.files(fastq_path,pattern=".fastq",full.names = T)
data.frame(fn=fn2,stringsAsFactors = F) %>%
mutate(ID=fn2 %>% sub(".*/","",.) %>% sub("\\..*","",.)
,R12=strsplit(fn2,"\\.") %>% sapply(intersect,y=c("R1","R2"))
) %>% acast(ID~R12,value.var="fn") %>% return()
}
check_soft=function(){
return(list(mothur_ver=system('mothur "#quit()"',intern = T) %>% "["(nchar(.)!=0)
,usearch_ver=system('usearch',intern = T) %>% "["(nchar(.)!=0)))
}
mothur.summary=function(x){
x %>%
"["(regexpr("\t",.)!=-1) %>%
strsplit("\t") %>% lapply(function(x){
if(length(x)!=8){
return(c("",x,rep("",7-length(x))))
} else {
return(x)
}
}) %>% do.call(rbind,.)
}
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