agat_sq_add_locus_tag.pl#

DESCRIPTION#

Add a shared locus tag per record. A record is all features linked by each other by parent/children relationship (e.g Gene,mRNA,exon, CDS).

agat_sq_add_locus_tag.pl --gff <input file> [-o <output file>]
agat_sq_add_locus_tag.pl --help

--gff, --file or --input

STRING: Input GTF/GFF file.
-p, --type or -l

Primary tag option, case insensitive, list. Allow to specied the Level1 feature types that will be handled. By default all feature Level1 are taken into account.
--lo or --to

Locus tag output, by defaut it will be called locus_tag, but using this option you can specied the name of this attribute.
--li or --ti

Tag input, by default the value of the locus tag attribute will be locusX where X is an incremented number. You can use the values of an existing attribute instead e.g the ID value: --li ID.
--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.
-q or --quiet

To remove verbosity.
-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.