seq_gtf: Get transcript sequences from GTF file and sequence info
In alyssafrazee/polyester-release: Simulate RNA-seq reads

Description Usage Arguments Value References Examples

Given a GTF file (for transcript structure) and DNA sequences, return a DNAStringSet of transcript sequences

1 2	seq_gtf(gtf, seqs, exononly = TRUE, idfield = "transcript_id", attrsep = "; ")

`gtf`	one of path to GTF file, or data frame representing a canonical GTF file.
`seqs`	one of path to folder containing one FASTA file (`.fa` extension) for each chromosome in `gtf`, or named DNAStringSet containing one DNAString per chromosome in `gtf`, representing its sequence. In the latter case, `names(seqs)` should contain the same entries as the `seqnames` (first) column of `gtf`.
`exononly`	if `TRUE` (as it is by default), only create transcript sequences from the features labeled `exon` in `gtf`.
`idfield`	in the `attributes` column of `gtf`, what is the name of the field identifying transcripts? Should be character. Default `"transcript_id"`.
`attrsep`	in the `attributes` column of `gtf`, how are attributes separated? Default `"; "`.

DNAStringSet containing transcript sequences, with names corresponding to idfield in gtf

http://www.ensembl.org/info/website/upload/gff.html

library(Biostrings)
  load(url('http://biostat.jhsph.edu/~afrazee/chr22seq.rda'))
  data(gtf_dataframe)
  chr22_processed = seq_gtf(gtf_dataframe, chr22seq)