gff3_sort.md

gff3-sort.py

Sort features in a gff3 file by according to their order on a scaffold, their coordinates on a scaffold, and parent-child relationships.

Inputs:

1. GFF3 file: Specify the file name with the -g argument

Outputs:

1. Sorted GFF3 file: Specify the file name with the -og argument
   • All related features (with parent-child relationships) are separated by ### directives for easier downstream parsing

Usage:

1. Specify the input, output file names and options using short arguments:
   • python2.7 bin/gff3_sort.py -g example_file/example.gff3 -og example_file/example_sorted.gff
2. Specify the input, output file names and options using long arguments:
   • python2.7 bin/gff3_sort.py --gff_file example_file/example.gff3 --output_gff example_file/example_sorted.gff

Optional arguments:

1. -h, --help
   • show this help message and exit
2. -g GFF_FILE, --gff_file GFF_FILE
   • GFF3 file that you would like to sort.
3. -og OUTPUT_GFF, --output_gff OUTPUT_GFF
   • Sorted GFF3 file
4. -v, --version
   • show program's version number and exit