--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_gff.R	Thu May 19 08:23:55 2022 +0000
@@ -0,0 +1,115 @@
+#!/usr/bin/env Rscript
+# function from questionr R package:
+wtable <- function(x, y = NULL, weights = NULL, digits = 3, normwt = FALSE, useNA = c("no", "ifany", "always"), na.rm = TRUE, na.show = FALSE, exclude = NULL)
+{
+  if (is.null(weights)) {
+    warning("no weights argument given, using uniform weights of 1")
+    weights <- rep(1, length(x))
+  }
+  if (length(x) != length(weights)) stop("x and weights lengths must be the same")
+  if (!is.null(y) & (length(x) != length(y))) stop("x and y lengths must be the same")
+  miss.usena <- missing(useNA)
+  useNA <- match.arg(useNA)
+  weights[is.na(weights)] <- 0
+  if (normwt) {
+    weights <- weights * length(x)/sum(weights)
+  }
+
+  if (!missing(na.show) || !missing(na.rm)) {
+    warning("'na.rm' and 'na.show' are ignored when 'useNA' is provided.")
+  }
+  if (useNA != "no" || (na.show && miss.usena)) {
+    if (match(NA, exclude, nomatch = 0L)) {
+      warning("'exclude' containing NA and 'useNA' != \"no\"' are a bit contradicting")
+    }
+    x <- addNA(x)
+    if (!is.null(y)) y <- addNA(y)
+  }
+  if (useNA == "no" || (na.rm && miss.usena)) {
+     s <- !is.na(x) & !is.na(weights)
+     if (!is.null(y)) s <- s & !is.na(y)
+     x <- x[s, drop = FALSE]
+     if (!is.null(y)) y <- y[s, drop = FALSE]
+     weights <- weights[s]
+  }
+  if (!is.null(exclude)) {
+    s <- !(x %in% exclude)
+    if (!is.null(y)) s <- s & !(y %in% exclude)
+    x <- factor(x[s, drop = FALSE])
+    if (!is.null(y)) y <- factor(y[s, drop = FALSE])
+    weights <- weights[s]
+  }
+  if (is.null(y)) {
+    result <- tapply(weights, x, sum, simplify = TRUE)
+  }
+  else {
+    result <- tapply(weights, list(x,y), sum, simplify = TRUE)
+  }
+  result[is.na(result)] <- 0
+  tab <- as.table(result)
+  if (useNA == "ifany") {
+    if (!is.null(y)) {
+      if (sum(tab[,is.na(colnames(tab))]) == 0) tab <- tab[,!is.na(colnames(tab))]
+      if (sum(tab[is.na(rownames(tab)),]) == 0) tab <- tab[!is.na(rownames(tab)),]
+    } else {
+      if (tab[is.na(names(tab))] == 0) tab <- tab[!is.na(names(tab))]
+    }
+  }
+  tab
+}
+
+suppressPackageStartupMessages(library(rtracklayer))
+library(parallel)
+g1 <- import(commandArgs(T)[1], format = "GFF")
+g2 <-  import(commandArgs(T)[2], format = "GFF")
+# assume non inrarange overlaps!
+attribute_name <- commandArgs(T)[3]
+if (FALSE){
+  g1 <- import("test_data/RM_LTR_TE.gff3")
+  g2 <- import("test_data/RM_RE.gff3")
+  g2 <- import("test_data/RM_RE_CL.gff3")
+  g2 <- import("test_data/RM_RE_v3.gff3")
+  g2 <- import("test_data/RM_RE_v4.gff3")
+
+  attribute_name <- "Name"
+}
+
+g1$SOURCE <- 1
+g2$SOURCE <- 2
+
+g12 <-  append(g1,g2)
+g12_disjoin <- disjoin(g12, ignore.strand=TRUE, with.revmap=TRUE)
+
+g12$sel_attr <- mcols(g12)[,attribute_name]
+
+annot_name <- mclapply(as.list(g12_disjoin$revmap), FUN = function(x)g12$sel_attr[x], mc.cores = 8)
+annot_source <- mclapply(as.list(g12_disjoin$revmap), FUN = function(x)g12$SOURCE[x], mc.cores = 8)
+
+c1 <- sapply(annot_source, function (x) 1 %in% x & !(2 %in% x))
+c2 <- sapply(annot_source, function (x) 2 %in% x & !(1 %in% x))
+c12 <- !(c1 | c2)
+
+
+n1 <- cbind(sapply(annot_name[c1], "[", 1 ), "No Annotation")
+n2 <- cbind("No Annotation", sapply(annot_name[c2], "[", 1))
+
+n12 <- do.call(rbind, annot_name[c12])
+
+n12all <- matrix(character(), ncol = 2, nrow = length(g12_disjoin))
+n12all[c1,] <- n1
+n12all[c2,] <- n2
+n12all[c12,] <- n12
+
+traw <- wtable(n12all[,1], n12all[,2], weights = width(g12_disjoin))
+tbl_df <- as.data.frame((traw))
+tbl_df <- tbl_df[order(tbl_df$Freq, decreasing = TRUE),]
+colnames(tbl_df) <-  c("Annotation1", "Annotation2", "Overlap[bp]")
+
+## NOTE - if name change - modify it in xml too
+write.table(tbl_df, file = 'annotation_overlap_long.csv', sep="\t", quote=FALSE, row.names = FALSE)
+
+tbl <- as.matrix(traw)
+tbl <- tbl[order(rowSums(tbl), decreasing = TRUE),]
+tbl <- tbl[, order(colSums(tbl), decreasing = TRUE)]
+write.table(tbl, file= 'annotation_overlap.csv', sep="\t", quote = FALSE)
+