library(rtracklayer)
gtf <- import("Homo_sapiens.GRCh37.87.chr.gtf.gz")
gtf <- gtf[gtf$gene_name!=""]
gtf <- gtf[!is.na(gtf$gene_name)]
## protein coding
protein <- 
  gtf$gene_name[gtf$transcript_biotype %in% 
                  c("IG_C_gene", "IG_D_gene", "IG_J_gene", "IG_LV_gene", 
                    "IG_M_gene", "IG_V_gene", "IG_Z_gene", 
                    "nonsense_mediated_decay", "nontranslating_CDS", 
                    "non_stop_decay", "polymorphic_pseudogene", 
                    "protein_coding", "TR_C_gene", "TR_D_gene", "TR_gene", 
                    "TR_J_gene", "TR_V_gene")]
## mitochondrial genes

mito <- gtf$gene_name[as.character(seqnames(gtf)) %in% "MT"]
## long noncoding
lincRNA <- 
  gtf$gene_name[gtf$transcript_biotype %in% 
                  c("3prime_overlapping_ncrna", "ambiguous_orf", 
                    "antisense_RNA", "lincRNA", "ncrna_host", "non_coding", 
                    "processed_transcript", "retained_intron", 
                    "sense_intronic", "sense_overlapping")]
## short noncoding
sncRNA <- 
  gtf$gene_name[gtf$transcript_biotype %in% 
                  c("miRNA", "miRNA_pseudogene", "misc_RNA", 
                    "misc_RNA_pseudogene", "Mt_rRNA", "Mt_tRNA", 
                    "Mt_tRNA_pseudogene", "ncRNA", "pre_miRNA", 
                    "RNase_MRP_RNA", "RNase_P_RNA", "rRNA", "rRNA_pseudogene", 
                    "scRNA_pseudogene", "snlRNA", "snoRNA", 
                    "snRNA_pseudogene", "SRP_RNA", "tmRNA", "tRNA",
                    "tRNA_pseudogene", "ribozyme", "scaRNA", "sRNA")]
## pseudogene
pseudogene <- 
  gtf$gene_name[gtf$transcript_biotype %in% 
                  c("disrupted_domain", "IG_C_pseudogene", "IG_J_pseudogene", 
                    "IG_pseudogene", "IG_V_pseudogene", "processed_pseudogene", 
                    "pseudogene", "transcribed_processed_pseudogene",
                    "transcribed_unprocessed_pseudogene", 
                    "translated_processed_pseudogene", 
                    "translated_unprocessed_pseudogene", "TR_J_pseudogene", 
                    "TR_V_pseudogene", "unitary_pseudogene", 
                    "unprocessed_pseudogene")]
annotations <- list(protein=unique(protein), 
                    mito=unique(mito),
                    lincRNA=unique(lincRNA),
                    sncRNA=unique(sncRNA),
                    pseudogene=unique(pseudogene))
annotations <- annotations[lengths(annotations)>0]