gff3_fix readme

Usage

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

Testing environment

Python 3.9+

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