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.