add possibility to generate txdb object from gtf file in diffbind2.R

tools/diffbind/diffbind2.R

@@ -88,9 +88,19 @@ if(!is.numeric(FOLD))        stop("Fold threshold is not numeric. Run with:\n",r
 if(!is.logical(ANNOTATE))    stop("Annotate not logical. Run with:\n",runstr)
 if(!is.logical(PE))          stop("Paired end (pe) not logical. Run with:\n",runstr)
 if(ANNOTATE & !is.numeric(TSS)) stop("Region around TSS not numeric. Run with:\n",runstr)
-if(ANNOTATE & !require(TXDB, character.only=TRUE))   stop("Transcript DB", TXDB, "not installed\n")
 if(ANNOTATE & !require(ANNODB, character.only=TRUE)) stop("Annotation DB", ANNODB, "not installed\n")
 
+if(ANNOTATE) {
+  if(grepl("\\.gtf$", TXDB)){ # check the input format for the transcript annotation
+    library(GenomicFeatures)
+    txdb <- makeTxDbFromGFF(TXDB, format="gtf") # if the input format is gtf file, then this file will be used to create a TxDb object
+  } else {
+    if(!require(TXDB, character.only=TRUE)) stop("Transcript DB", TXDB, "not installed\n")
+    txdb <- eval(parse(text=TXDB)) # if the input format is bioconductor, then the transcript annoation library will be used 
+  }
+}
+
+
 # check for DiffBind version
 currentDiffbindVersion <- packageVersion('DiffBind')
 DiffBindWarningText <- ""
@@ -285,7 +295,6 @@ dev.off()
 ##
 if(ANNOTATE) {
   library(ChIPseeker)
-  txdb <- eval(parse(text=TXDB))
   result <- lapply(result, function(x) {
     tryCatch({
       x.ann <- annotatePeak(x, TxDb=txdb, annoDb=ANNODB, tssRegion=TSS, verbose=T)