gff3_fix readme

Usage

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

Testing environment

Python 2.7

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

python2.7 bin/gff3_fix.py -qc_r error.txt -g example.gff3 -og corrected.gff3

Optional arguments

  1. -h, –help
    • show this help message and exit
  2. -og OUTPUT_GFF, –output_gff OUTPUT_GFF
    • output gff3 file name
  3. -v, –version
    • show program’s version number and exit