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agat_sp_Prokka_inferNameFromAttributes.pl#

DESCRIPTION#

The script aims to fill a Name attribute based on <gene> attribute in a prokka gff annotation file. If no gene attribute is present it take if from the <inference> attribute.

SYNOPSIS#

agat_sp_Prokka_inferNameFromAttributes.pl -gff file.gff  [ -o outfile ]
agat_sp_Prokka_inferNameFromAttributes.pl --help

OPTIONS#

  • --gff or -f

    Input GTF/GFF file.

  • --force

    If Name attribute already exists, they will be replaced if a new one is found

  • -o , --output , --out or --outfile

    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.