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agat_sq_list_attributes.pl#

DESCRIPTION#

The script take a gff3 file as input. - The script give information about attribute tags used within you file.

SYNOPSIS#

agat_sq_list_attributes.pl -gff file.gff -p level2,cds,exon [ -o outfile ]
agat_sq_list_attributes.pl --help

OPTIONS#

  • --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.

  • -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.