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.

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