R_gtf_formater

####### Transfer codon information from tRNA_codons to tRNA_GTF

#### it seems that the two annotation files have no common areas, write a GTF file using the tRNA-codons file
# file.create('tRNA_gtf_gtRNAdb.txt')
# for (i in 1:nrow(tRNA_codons)){
#     cat(tRNA_codons[i,3], file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('ENSEMBL', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('tRNA', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat(tRNA_codons[i,5], file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat(tRNA_codons[i,6], file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('.', file='tRNA_gtf_gtRNAdb.txt', append=TRUE) 
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat(tRNA_codons[i,4], file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('.', file='tRNA_gtf_gtRNAdb.txt', append=TRUE) 
#     cat('\t', file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat(paste0('gene_id ', paste0('\"tRNA',as.character(i),'\"', ';'),
#                 ' transcript_id ', paste0('\"tRNA',as.character(i),'\"', ';'),
#                 ' gene_type ', paste0('\"tRNA\"', ';'), 
#                 ' gene_status ', paste0('\"NULL\"', ';'), 
#                 ' gene_name ', paste0('\"tRNA',as.character(i),'\"', ';'), 
#                 ' transcript_type ', paste0('\"tRNA\"', ';'), 
#                 ' transcript_status ', paste0('\"NULL\"', ';'), 
#                 ' transcript_name ', paste0('\"tRNA',as.character(i),'\"', ';'), 
#                 ' level ',paste0(3, ';')), file='tRNA_gtf_gtRNAdb.txt', append=TRUE)
#     cat('\n', file='tRNA_gtf_gtRNAdb.txt',append=TRUE)
# }

#### GTF file made from lifted coordinates does not have many reads map to it(roughly 20% the amount when using ENCODE tRNA GTF file)