agat_sp_fix_cds_frame.pl

DESCRIPTION

This script aims to fix the cds phases.

SYNOPSIS

agat_sp_fix_cds_frame.pl --gff infile.gff -f fasta [ -o outfile ]
agat_sp_fix_cds_frame.pl --help

OPTIONS

  • -g, --gff or -ref

    Input GTF/GFF file.

  • -fa or --fasta

    Input fasta file.

  • -v or --verbose

    Add verbosity.

  • -o or --output

    Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -h or --help

    Display this helpful text.