build_genome_feature gff red upgrade

R/build_genome_features.R

@@ -410,8 +410,17 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
   ###################
   # read the gff
-  gff<-data.table::fread(file,fill=T,drop=base::c(2,6,8),verbose=F,showProgress=F,col.names=base::c("chr",
-  "type","start","end","strand","att"))[data.table::like(type,"RNA|transcript") & !data.table::like(chr,"^#")]
+  #gff<-data.table::fread(file,fill=T,drop=base::c(2,6,8),verbose=F,showProgress=F,col.names=base::c("chr",
+  #"type","start","end","strand","att"))[data.table::like(type,"RNA|transcript") & !data.table::like(chr,"^#")]
+  
+  gff<-data.table::fread(file,sep="",verbose=F,showProgress=F,header=F)[data.table::like(base::gsub("ID=.+$","",V1),"[[:space:]].+(RNA|transcript)"),]
+  
+  ###################
+  # parse it
+  gff<-gff[,{
+    tmp=data.table::data.table(base::t(base::strsplit(V1,"\t")[[1]]));
+    base::list(chr=tmp$V1,type=tmp$V3,start=tmp$V4,end=tmp$V5,strand=tmp$V7,att=tmp$V9)
+    },by=1:base::nrow(gff)][,base:=NULL]
 
   ###################
   # remove files