add utils from TE_Aalb repo

Author: TommasoBarberis

utils/query_coverage.R

@@ -0,0 +1,35 @@
+#!/usr/bin/Rscript
+
+# https://github.com/clemgoub/TE-Aid/blob/master/consensus2genome.R
+# https://github.com/clemgoub/TE-Aid/blob/master/Run-c2g.R
+
+Args 		    =	commandArgs()
+blast_file		=	Args[6]
+cons_len        =   as.numeric(Args[7])
+out_file        =   as.character(Args[8])
+
+cons_coverage=function(blast_file=NULL, cons_len=NULL, out_file=NULL){
+    blast = read.table(blast_file, sep="\t")
+    new_rownames <- c(paste(blast$V2,"-",as.character(blast$V8),":",as.character(blast$V9), sep = ""))
+
+    #make the coverage matrix
+    coverage = matrix(rep(0, length(blast$V1)*as.numeric(cons_len)), byrow = T, ncol = as.numeric(cons_len))
+    for(i in 1:length(blast$V1)){
+        if (blast$V7[i] <= cons_len) {
+            coverage[i,]<-c(rep(0, blast$V6[i]-1),rep(1, abs(blast$V7[i]-blast$V6[i])+1), rep(0, as.numeric(cons_len)-blast$V7[i]))
+        }
+    }
+    
+    rownames(coverage) <- new_rownames
+    coverage<-colSums(coverage)
+    write.table(coverage, file=out_file, col.names=F, row.names=F)
+
+    # number of full copies
+    full=blast[abs(blast$V6-blast$V7) >= 0.9*as.numeric(cons_len),]
+    cat(nrow(full))    
+}
+
+cons_coverage(blast_file = blast_file,
+    cons_len = cons_len,
+    out_file = out_file
+)