gff3_fix readme¶
Usage¶
gff3_fix.py [-h] [-qc_r QC_REPORT] [-g GFF] [-og OUTPUT_GFF] [-v]
Testing environment¶
Python 3.x
Inputs¶
- 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.
- GFF3: Specify the file name with the -g or –gff argument.
Outputs¶
- Corrected GFF3
Quick start¶
gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3
Optional arguments¶
- -h, –help
- show this help message and exit
- -qc_r QC_REPORT, –qc_report QC_REPORT
- Error report from gff3_QC.py
- -g GFF, –gff GFF
- Genome annotation file, gff3 format
- -og OUTPUT_GFF, –output_gff OUTPUT_GFF
- output gff3 file name (default: corrected.gff3)
- -v, –version
- show program’s version number and exit