added gtf support

src/R/createSyntheticTranscripts.R

-"createSyntheticTranscripts" <- function(gff3,
-                                         output = c("Genome_intervals","GRanges"),
-                                         features = c("mRNA", "tRNA", "miRNA")) {
-  require(genomeIntervals)
-  require(S4Vectors)
-
+"createSyntheticTranscripts" <- function(filename,
+                                         input = c("gff3","gtf"),
+                                         features = c("mRNA", "miRNA", "tRNA", "transcript"),
+                                         output = c("Genome_intervals","GRanges")) {
+
+  #' load libraries
+  stopifnot(require(genomeIntervals))
+  stopifnot(require(S4Vectors))
+  stopifnot(require(IRanges))
+  stopifnot(require(easyRNASeq))
+
+  #' first check
+  stopifnot(file.exists(filename))
+
+  #' get the values
+  input <- match.arg(input)
   features <- match.arg(features, several.ok = TRUE)
   output <- match.arg(output)
 
-  gff <- readGff3(gff3)
+  #' define some global variables
+  relation <- switch(input,
+                     "gff3"=list(ID="ID",Parent="Parent"),
+                     "gtf"=list(ID="transcript_id",Parent="gene_id"))
+
+  #' read the gff3/gtf file
+  dat <- readGff3(filename)
 
-  ## get the gene <-> pacid map
+  #' If gtf, reformat the attributes and drop the double quotes
+  if(input=="gtf"){
+    dat$gffAttributes <- gsub("\"","",easyRNASeq:::.convertGffToGtfAttributes(dat$gffAttributes))
+  }
+
+  ## get the gene <-> mRNA/transcript 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"))
+  sel <- dat$type %in% features
+
+  # That step would not necessary for gtf, but it is easier to implement in a
+  # similar way for both format
+  idMap <- data.frame(type = dat[sel]$type,
+                      getGffAttribute(dat[sel],relation$ID),
+                      getGffAttribute(dat[sel],relation$Parent))
 
   ## extract the exons and group by gene ID
-  sel <- gff$type == "exon"
+  sel <- dat$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"))
+  mRnaID <- sub(",.*","",getGffAttribute(dat[sel],switch(input,
+                                                         "gff3"=relation$Parent,
+                                                         "gtf"=relation$ID)))
 
   ## avoid unwanted features
-  rngs <- IRanges::IRanges(start = gff[sel, 1],
-                           end = gff[sel, 2])[mRnaID %in% idMap$ID]
+  rngs <- IRanges(start = dat[sel, 1],
+                  end = dat[sel, 2])[mRnaID %in% idMap[,relation$ID]]
 
   ## create a set of synthetic exons
   rngList <- IRanges::reduce(
     IRanges::split(rngs,
-                   idMap[match(mRnaID[mRnaID %in% idMap$ID],
-                               idMap$ID),"Parent"]))
+                   idMap[match(mRnaID[mRnaID %in% idMap[,relation$ID]],
+                               idMap[,relation$ID]),relation$Parent]))
 
   ## export the gene, exon and features as gff3
   ## create the new gff object
   ## select the gene
-  sel <- gff$type == "gene"
+  sel <- dat$type == "gene"
 
   ## create the gene gff
-  geneID <- getGffAttribute(gff[sel],"ID")
-  geneGff <- gff[sel][geneID %in% idMap$Parent]
+  geneID <- getGffAttribute(dat[sel],switch(input,
+                                            "gff3"=relation$ID,
+                                            "gtf"=relation$Parent))
+  geneGff <- dat[sel][geneID %in% idMap[,relation$Parent]]
+  if (input == "gtf"){
+    geneGff$gffAttributes <- sub(relation$Parent,"ID",geneGff$gffAttributes)
+  }
 
   ## create gffs for each feature
   featureGff <- Reduce(c, lapply(features, function(f) {
-    fGff <- gff[sel][geneID %in% idMap$Parent[idMap$type == f]]
+    f.sel <- geneID %in% idMap[,relation$Parent][idMap$type == f]
+    fGff <- dat[sel][f.sel]
     fGff$type <- f
-    fGff$gffAttributes <- paste(paste(
-      sub(";", ".0;", fGff$gffAttributes), "0;Parent=", sep="."),
-      geneID[geneID %in% idMap$Parent[idMap$type == f]], sep="")
+    fGff$gffAttributes <- paste("ID=",
+                                getGffAttribute(fGff,relation$Parent),
+                                ".0;Parent=",
+                                getGffAttribute(fGff,relation$Parent),
+                                sep="")
     fGff
   }))
 
   ## create the exon gff
-  rngList <- rngList[match(geneID[geneID %in% idMap$Parent], names(rngList))]
+  rngList <- rngList[match(geneID[geneID %in% idMap[,relation$Parent]], names(rngList))]
   exonNumber <- elementLengths(rngList)
-  exonGff <- gff[rep(which(sel)[geneID %in% idMap$Parent], exonNumber)]
+  exonGff <- dat[rep(which(sel)[geneID %in% idMap[,relation$Parent]], exonNumber)]
   exonGff[,1] <- IRanges::unlist(start(rngList))
   exonGff[,2] <- IRanges::unlist(end(rngList))
 
   exonID <- sapply(exonNumber, ":", 1)
   sel <- geneGff$strand == "+"
   exonID[sel] <- sapply(exonID[sel], rev)
-  ID <- getGffAttribute(exonGff, "ID")
+  ID <- getGffAttribute(exonGff, switch(input,"gff3"=relation$ID,"gtf"=relation$Parent))
   exonGff$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 = "."))