instructions create genome position file

Making a Genomic Position File

To generate a Genomic Positions file from a GTF file please use the gtf_to_position_file.py script provided in the scripts directory.

# By Default use gene_id as the name of your feature
python ./scripts/gtf_to_position_file.py your_reference.gtf your_gen_pos.txt

# You can change what gtf attribute key is used, here transcript_id is used.
python ./scripts/gtf_to_position_file.py --attribute_name transcript_id your_reference.gtf your_gen_pos.txt

(This command should work in both Python 2.X and 3.X environments).