Kraken style mpa report about centrifuge HOT 4 OPEN

# Create file for the OTU count
Computer:~$ cut -f2- Merged_File.txt >  Merged_file_OTU.txt

#Create file for Taxonomy
Computer:~$ cut -f1  Merged_File.txt > Merged_file_TAX.txt

library(phyloseq)
otumat=read.table("Merged_file_OTU.txt",fill=TRUE,header=TRUE,check.names = F)

#Convert table to matrix
otumat<-as.matrix(otumat)

#Count the depth of taxonomy
nc<-max(count.fields("Merged_file_TAX.txt",sep="|"))


#Use the count in previous step to fill in the RANKS as R1,R2  and so forth
tax<-read.table(" Merged_file_TAX.txt",sep="|",col.names = paste("R",1:nc,sep=""),fill=T)

#Convert table to matrix
taxmat<-as.matrix(tax)

#Number your rows as OTUs
rownames(otumat)<-paste0("OTU",1:nrow(otumat))

#This makes sure that both the OTUs and Taxnomy have same row ids
rownames(taxmat)<-rownames(otumat)

#Creates OTU table for Phyloseq
OTU<-otu_table(otumat,taxa_are_rows = T)

#Create taxnomy table for phyloseq
TAX<-tax_table(taxmat)


#This is where you get the phyloseq object
physeq=phyloseq(OTU,TAX)


#Load optional meta data (This is must for anything meaningful)
samat=read.table("Metadata.tsv")

#Merge sample metadata with the phyloseq object
physeq_with_samples<-merge_phyloseq(physeq,sample_data(data.frame(samat)))


#Save the data for later use so we don't have to repeat the above steps
save(physeq_with_samples,file="phyobject.rda")