agat_sq_manage_ID.pl#
DESCRIPTION#
The script changes IDs to give uniq one and reflect the change in Parent attribute of impacted features.
SYNOPSIS#
agat_sq_manage_IDs.pl --gff <input file> [-o <output file>]
agat_sq_manage_IDs.pl --help
OPTIONS#
-
--gff, --file or --input
STRING: Input GTF/GFF file.
-
--of
Output format, if no ouput format is given, the same as the input one detected will be used. Otherwise you can force to have a gff version 1 or 2 or 3 by giving the corresponding number.
-
-o or --output
STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.
-
-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).
-
--help or -h
Display this helpful text.