gff3_sort readme¶
Sort features in a gff3 file by according to their order on a scaffold, their coordinates on a scaffold, and parent-child relationships.
Inputs:¶
- GFF3 file: Specify the file name with the -g argument
Outputs:¶
- 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
- All related features (with parent-child relationships) are separated by
Usage:¶
- 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
- 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:¶
- -h, –help
- show this help message and exit
- -g GFF_FILE, –gff_file GFF_FILE
- GFF3 file that you would like to sort.
- -og OUTPUT_GFF, –output_gff OUTPUT_GFF
- Sorted GFF3 file
- -v, –version
- show program’s version number and exit
Assumptions:¶
- Any features without a Parent attribute are ‘root’ features - the program will insert directives (lines beginning with ##) above these features.
- All child features occur after their respective Parent feature, but before new Parent features.