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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

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