01_MergeTables

setwd("~/AlgaeProject/Nannochloropsis/outputs/")

# extract the files containing "renamed"
DIR=dir(path = ".",pattern = "renamed", full.names = T)

# generate starting point for the collector table
abundPath=dir(DIR[1] ,"tsv", full.names = T)
temp=read.table(abundPath, header = T)
collector=temp[,c(1,4)]
head(collector)

# generate collector table
for(i in DIR[-1] ){
  print(i)
  abundPath=dir(i,"tsv", full.names = T)
  temp=read.table(abundPath, header =T )
  print(all(temp[,1] == collector[,1]  ))
  collector=cbind(collector,temp[,4] )
} 
head(collector)

#rename to sample names
colnames(collector) =c("feat",basename(DIR))
head(collector)

# round off reads to integers
collector[,2:ncol(collector)] <- round(collector[,2:ncol(collector)], digits=0)
head(collector)

write.csv(collector,"~/AlgaeProject/Nannochloropsis/Scripts/MergeTables_collector_cds.csv", row.names = F)