gff3_fix.md

gff3_fix readme

Usage

gff3_fix.py [-h] [-qc_r QC_REPORT] [-g GFF] [-og OUTPUT_GFF] [-v]

Testing environment

Python 3.x

Inputs

1. Error report: Error report from gff3_QC.py. Specify the file name with the -qc_r or --qc_report argument. Error report should only include those errors that should be fixed. If errors identified by gff3_QC.py should not be fixed, remove lines containing errors from report file.
2. GFF3: Specify the file name with the -g or --gff argument.

Outputs

1. Corrected GFF3

Quick start

gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3

Optional arguments

1. -h, --help
   • show this help message and exit
2. -qc_r QC_REPORT, --qc_report QC_REPORT
   • Error report from gff3_QC.py
3. -g GFF, --gff GFF
   • Genome annotation file, gff3 format
4. -og OUTPUT_GFF, --output_gff OUTPUT_GFF
   • output gff3 file name (default: corrected.gff3)
5. -v, --version
   • show program's version number and exit

More information

• gff3_fix.py full documentation