#!/usr/bin/Rscript

brca_file <- "/home/zhanghl/workshop/paper1/expression/survival_gene_analysis/310_down_genes/BRCA.survival.sf"
kirc_file <- "/home/zhanghl/workshop/paper1/expression/survival_gene_analysis/310_down_genes/KIRC.survival.sf"
prad_file <- "/home/zhanghl/workshop/paper1/expression/survival_gene_analysis/310_down_genes/PRAD.survival.sf"
thca_file <- "/home/zhanghl/workshop/paper1/expression/survival_gene_analysis/310_down_genes/THCA.survival.sf"
ucsc_file <- "/home/zhanghl/workshop/paper1/expression/survival_gene_analysis/310_down_genes/UCEC.survival.sf"

brca <- read.table(brca_file,header=FALSE,sep=" ",stringsAsFactors=FALSE)
kirc <- read.table(kirc_file,header=FALSE,sep=" ",stringsAsFactors=FALSE)
prad <- read.table(prad_file,header=FALSE,sep=" ",stringsAsFactors=FALSE)
thca <- read.table(thca_file,header=FALSE,sep=" ",stringsAsFactors=FALSE)
ucsc <- read.table(ucsc_file,header=FALSE,sep=" ",stringsAsFactors=FALSE)

brca_genes <- brca[brca[,6]<=0.05 & brca[,8]>1,4]
kirc_genes <- kirc[kirc[,6]<=0.05 & kirc[,8]>1,4]
prad_genes <- prad[prad[,6]<=0.05 & prad[,8]>1,4]
thca_genes <- thca[thca[,6]<=0.05 & thca[,8]>1,4]
ucsc_genes <- ucsc[ucsc[,6]<=0.05 & ucsc[,8]>1,4]

mylist <- list(brca_genes,kirc_genes,prad_genes,thca_genes,ucsc_genes)

one_tumor_sig <- unique(c(brca_genes,kirc_genes,prad_genes,thca_genes,ucsc_genes))
               
               two_tumor_sig <- c()
               for (i in one_tumor_sig){
                   v=0
                   for (j in 1:length(mylist)) {
                       len <- ifelse(  length(intersect(i,mylist[[j]]))>0  ,1,0) ; v <- v+len
                   }
                       gene <- ifelse(v>=2,i,"NA"); print(gene);two_tumor_sig <- c(two_tumor_sig,gene)
               }
               
               two_tumor_sig <- two_tumor_sig[two_tumor_sig!="NA"]
                               
               
               three_tumor_sig <- c()
                   for (i in one_tumor_sig){
                   v=0
                   for (j in 1:length(mylist)) {
                       len <- ifelse(  length(intersect(i,mylist[[j]]))>0  ,1,0) ; v <- v+len
                   }
                       gene <- ifelse(v>=3,i,"NA"); three_tumor_sig <- c(three_tumor_sig,gene)
               }
               
               three_tumor_sig <- three_tumor_sig[three_tumor_sig!="NA"]
               
                               
               four_tumor_sig <- c()
               for (i in one_tumor_sig){
                   v=0
                   for (j in 1:length(mylist)) {
                       len <- ifelse(  length(intersect(i,mylist[[j]]))>0  ,1,0) ; v <- v+len
                   }
                       gene <- ifelse(v>=4,i,"NA"); four_tumor_sig <- c(four_tumor_sig,gene)
               }
               four_tumor_sig <- four_tumor_sig[four_tumor_sig!="NA"]
               
               
               
               five_tumor_sig <- c()
               for (i in one_tumor_sig){
                   v=0
                   for (j in 1:length(mylist)) {
                       len <- ifelse(  length(intersect(i,mylist[[j]]))>0  ,1,0) ; v <- v+len
                   }
                       gene <- ifelse(v>=5,i,"NA"); print(gene); five_tumor_sig <- c(five_tumor_sig,c)
               }
               five_tumor_sig <- five_tumor_sig[five_tumor_sig!="NA"]