library('getopt')
suppressPackageStartupMessages(library('phyloseq'))
suppressPackageStartupMessages(library('DESeq2'))

options(warn= -1)

option_specification = matrix(c(
   'biomfile','b',2,'character',
   'metafile','m',2,'character',
     'factor','f',2,'numeric',
       'test','t',2,'character',
    'fitType','T',2,'character',
     'cutoff','c','2','double',
     'outdir','o',2,'character',
   'result','r',2,'character',
   'normalisedResult','n','2','character'
),byrow=TRUE,ncol=4);


options <- getopt(option_specification);
options(bitmapType="cairo")
 

if (!is.null(options$outdir)) {
  # Create the directory
  dir.create(options$outdir,FALSE)
}


galaxy_biom <- import_biom(options$biomfile)
galaxy_map <- import_qiime_sample_data(options$metafile)
tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")

number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))

if( number.of.tax.rank == 7){
colnames(tax_table(galaxy_biom)) <- tax_col_norm
}else{
colnames(tax_table(galaxy_biom)) <- tax_col_extra
}


AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)


Infactor<-colnames(galaxy_map)[options$factor]
method<-options$test
Type<-options$fitType
cutoff<-options$cutoff



suppressMessages(deseq2_obj<-phyloseq_to_deseq2(AIP_galaxy,as.formula(paste('~',Infactor,sep=""))))
gm_mean = function(x, na.rm=TRUE){
  exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
}
geoMeans = apply(counts(deseq2_obj), 1, gm_mean)
deseq2_obj = estimateSizeFactors(deseq2_obj, geoMeans = geoMeans)



### Normalisation
deseq2_obj_norm<-counts(deseq2_obj,normalized=T)
deseq2_obj_norm.out<-as.data.frame(cbind("OTUID"=rownames(deseq2_obj_norm),deseq2_obj_norm))
write.table(deseq2_obj_norm.out,file=options$normalisedResult,col.names=T,row.names=F,quote=F,sep="\t")


### Normalisation and DE analysis
suppressMessages(deseq2_obj_DE<-DESeq(deseq2_obj,test=method,fitType=Type))
res = results(deseq2_obj_DE,cooksCutoff = FALSE)

significant.table <-res[which(res$padj < cutoff),]

if(nrow(significant.table) == 0){
  out_message <-"no significant result found!"
  write(out_message,file=options$result,sep="\t")
  quit("yes")
}

significant.table <- cbind(as(significant.table,"data.frame"), as(tax_table(AIP_galaxy)[rownames(significant.table),],"matrix"))

significant.table.out<-as.data.frame(cbind("OTUID"=rownames(significant.table),significant.table))

write.table(format(significant.table.out, digits=4, scientific=F),file=options$result,col.names=T,row.names=F,quote=F,sep="\t")