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.