Create_Input_Table.R

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######                             Main Script                              ######
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###################       Load all required libraries     ########################

check_and_load <- function(package_name) {
  if (!package_name %in% rownames(installed.packages())) {
    cat(sprintf("The library '%s' is not installed.\n", package_name))
    # Optionally, you could install the package here if it is not found
  } else {
    tryCatch({
      library(package_name, character.only = TRUE)
      cat(sprintf("The library '%s' has been loaded successfully.\n", package_name))
    }, error = function(e) {
      cat(sprintf("Failed to load the library '%s': %s\n", package_name, e$message))
    })
  }
}

# Example usage
check_and_load("compare")

###################            Read input table              ####################

# Reading Alpha diversity file
alpha <- read.table(file=alpha,header=TRUE,sep="\t",row.names=1,check.names = F)

# Clean table from empty lines
alpha <- alpha[!apply(is.na(alpha) | alpha=="",1,all),]

# Read OTU table
RelativeAbundanceOTUs <-as.data.frame(t(read.table(file=RelativeAbundanceOTUs,header=TRUE,sep="\t",row.names = 1,check.names = F)))

# Clean table from empty lines
RelativeAbundanceOTUs <- RelativeAbundanceOTUs[!apply(is.na(RelativeAbundanceOTUs) | RelativeAbundanceOTUs=="",1,all),]

# Read Mapping file
MetaFile <- read.table(file=MetaFile,header=TRUE,sep="\t",comment.char = "",row.names = 1,check.names = F)

# Clean table from empty lines
MetaFile <- MetaFile[!apply(is.na(MetaFile) | MetaFile=="",1,all),,drop=FALSE]

# Read taxonomy file
TaxanomyAll <- read.table(file=TaxanomyAll,header=TRUE,sep="\t",row.names=NULL,check.names = F)

# Clean table from empty lines
TaxanomyAll <- TaxanomyAll[!apply(is.na(TaxanomyAll) | TaxanomyAll=="",1,all),]

# Select the RelativeAbundanceOTUs and alpha rows based on the mapping file
RelativeAbundanceOTUs <- RelativeAbundanceOTUs[rownames(MetaFile),]
alpha <- alpha[rownames(MetaFile),]

# Prepare TaxanomyAll table
ColnameTo_assign<- TaxanomyAll[,1]
TaxanomyAll[,1] <- NULL
TaxanomyAll <- as.data.frame(t(TaxanomyAll))
TaxanomyAll <- TaxanomyAll[rownames(MetaFile),]
colnames(TaxanomyAll) <- ColnameTo_assign

######################          MAIN PROGRAM                #####################

# Preparing TAXA table:
combine_taxa<- cbind.data.frame(MetaFile[rownames(TaxanomyAll),],alpha[rownames(TaxanomyAll),],TaxanomyAll) # merging Meta+Alpha+Taxa based on same order row.
combine_taxa$SampleID <- row.names(combine_taxa)
combine_taxa<-combine_taxa[,c(ncol(combine_taxa),1:(ncol(combine_taxa)-1))]# replacing columnn at the beginging.

# Prepare OTU table:
combine_OTUs<- cbind.data.frame(MetaFile[rownames(RelativeAbundanceOTUs),],alpha[rownames(RelativeAbundanceOTUs),],RelativeAbundanceOTUs) # merging Meta+Alpha+OTUs based on same order row.
combine_OTUs$SampleID <- row.names(combine_OTUs)
colnames(combine_OTUs)
combine_OTUs<-combine_OTUs[,c(ncol(combine_OTUs),1:(ncol(combine_OTUs)-1))]# replacing columnn at the beginging.

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######                        Write Output Files                           ######
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# Writing tables
if(compareIgnoreOrder(row.names(TaxanomyAll),row.names((MetaFile)))$result &
   compareIgnoreOrder(row.names(alpha),row.names((MetaFile)))$result &
   compareIgnoreOrder(row.names(RelativeAbundanceOTUs),row.names((MetaFile)))$result){
  write.table(combine_taxa,file="TaxaCombined.tab",sep="\t",row.names=FALSE)
  write.table(combine_OTUs,file="OTUsCombined.tab",sep="\t",row.names=FALSE)
  message("Files are combined successfully")
}else{
  stop("ATTENTION !!!! Sample names differ across files. Script aborted.",
       "Please ensure that identical sample names are used.")
}



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######                           End of Script                             ######
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