The script takes a gtf/gff file as input. The script allows to extract choosen attributes of all or specific feature types. The 9th column of a gff/gtf file contains a list of attributes. An attribute (gff3) looks like that tag=value

SYNOPSIS -gff file.gff  -att locus_tag,product,name -p level2,cds,exon [ -o outfile ] --help


  • --gff or -f

    Input GTF/GFF file.

  • -p, -t or -l

    primary tag option, case insensitive, list. Allow to specied the feature types that will be handled. You can specified a specific feature by given its primary tag name (column 3) as: cds, Gene, MrNa You can specify directly all the feature of a particular level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By default all feature are taking in account. fill the option by the value "all" will have the same behaviour.

  • --attribute, --att, -a

    attribute tag. The value of the attribute tag specified will be extracted from the feature type specified by the option -p. List of attributes must be coma separated.

  • --merge or -m

    By default the values of each attribute tag is writen in its dedicated file. To write the values of all tags in only one file use this option.

  • -d

    By default when an attribute is not found for a feature, a dot (.) is reported. If you don't want anything to be printed in such case use this option.

  • -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.