A minimal tool for sequence extraction for every transcript (only from exonic regions) in a gtf from a fasta file.
It's written in Julia and has no dependencies. See here for Julia installation.
This tool requires indexed fasta file for memory efficient sequence extraction.
#Extracting fasta sequence from gtf file (sequences are written to stdout)
$ gtf2fasta.jl ens82.gtf hg19.fa | head
>ENST00000456328
GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA
GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA
GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG
...It will also generate ens82.gtf.transcript.dict.tsv with transcript to gene mappings.