seq_gtf: Get transcript sequences from GTF file and sequence info
In alyssafrazee/polyester: 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

seq_gtf(
  gtf,
  seqs,
  feature = "transcript",
  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`.
`feature`	one of `'transcript'` or `'exon'` (default transcript), depending on desired return.
`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 `"; "`.

If feature is 'transcript', DNAStringSet containing transcript sequences, with names corresponding to idfield in gtf. If feature is 'exon', DNAStringSet containing exon sequences from gtf, named by exon location (chr, start, end, strand).

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

 ## Not run: 
  library(Biostrings)
  system('wget https://www.dropbox.com/s/04i6msi9vu2snif/chr22seq.rda')
  load('chr22seq.rda')
  data(gtf_dataframe)
  chr22_processed = seq_gtf(gtf_dataframe, chr22seq)

## End(Not run)