Added a script to create synthetic transcripts. Modified execute permissions...

Added a script to create synthetic transcripts. Modified execute permissions for the RNASeq preprocessing runner

src/R/createSyntheticTranscripts.R

+"createSyntheticTranscripts" <- function(gff3,
+                                         output = c("Genome_intervals","GRanges"),
+                                         features = c("mRNA", "tRNA", "miRNA")) {
+  require(genomeIntervals)
+  require(S4Vectors)
+
+  features <- match.arg(features, several.ok = TRUE)
+  output <- match.arg(output)
+
+  gff <- readGff3(gff3)
+
+  ## get the gene <-> pacid map
+  # This is mRNA IDs and their parents (genes)
+  sel <- gff$type %in% features
+  idMap <- data.frame(type = gff[sel]$type,
+                      getGffAttribute(gff[sel],"ID"),
+                      getGffAttribute(gff[sel],"Parent"))
+
+  ## extract the exons and group by gene ID
+  sel <- gff$type == "exon"
+
+  ## we can drop multiple Parents (i.e. comma separated Parent values as we are
+  ## collapsing them anyway)
+  mRnaID <- sub(",.*","",getGffAttribute(gff[sel],"Parent"))
+
+  ## avoid unwanted features
+  rngs <- IRanges::IRanges(start = gff[sel, 1],
+                           end = gff[sel, 2])[mRnaID %in% idMap$ID]
+
+  ## create a set of synthetic exons
+  rngList <- IRanges::reduce(
+    IRanges::split(rngs,
+                   idMap[match(mRnaID[mRnaID %in% idMap$ID],
+                               idMap$ID),"Parent"]))
+
+  ## export the gene, exon and features as gff3
+  ## create the new gff object
+  ## select the gene
+  sel <- gff$type == "gene"
+
+  ## create the gene gff
+  geneID <- getGffAttribute(gff[sel],"ID")
+  geneGff <- gff[sel][geneID %in% idMap$Parent]
+
+  ## create gffs for each feature
+  featureGff <- Reduce(c, lapply(features, function(f) {
+    fGff <- gff[sel][geneID %in% idMap$Parent[idMap$type == f]]
+    fGff$type <- f
+    fGff$gffAttributes <- paste(paste(
+      sub(";", ".0;", fGff$gffAttributes), "0;Parent=", sep="."),
+      geneID[geneID %in% idMap$Parent[idMap$type == f]], sep="")
+    fGff
+  }))
+
+  ## create the exon gff
+  rngList <- rngList[match(geneID[geneID %in% idMap$Parent], names(rngList))]
+  exonNumber <- elementLengths(rngList)
+  exonGff <- gff[rep(which(sel)[geneID %in% idMap$Parent], exonNumber)]
+  exonGff[,1] <- IRanges::unlist(start(rngList))
+  exonGff[,2] <- IRanges::unlist(end(rngList))
+
+  exonID <- sapply(exonNumber, ":", 1)
+  sel <- geneGff$strand == "+"
+  exonID[sel] <- sapply(exonID[sel], rev)
+  ID <- getGffAttribute(exonGff, "ID")
+  exonGff$gffAttributes <- paste0("ID=", paste(ID, "exon", unlist(exonID, use.names=FALSE), sep="."),
+                                 ";Name=", paste(ID, "exon", unlist(exonID, use.names=FALSE), sep="."),
+                                 ";Parent=", paste(ID,"0",sep = "."))
+  exonGff$type <- "exon"
+
+  ## combine
+  newgff <- c(geneGff, featureGff, exonGff)
+
+  ## change the source
+  newgff$source <- "UPSC"
+
+  ## sort
+  newgff <- newgff[order(seq_name(newgff), newgff[, 1],
+                         factor(as.character(newgff$type),
+                                labels = seq_len(2 + length(features)),
+                                levels = c("gene", features, "exon"))), ]
+
+  return(switch(output,
+                "Genome_intervals" = newgff,
+                "GRanges" = as(newgff, "GRanges"),
+                stop(paste("Cannot generate output of type", output))))
+}