python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/gtf-to-fastaFromFasta.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-male.fa /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.fa