The script aims to keep records based on a keeplist. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the keeplist it will be kept along with all related features (the whole record is kept. A record repsent all features linked by relationship e.g. gene+transcript+exon+cds of a same locus).
agat_sp_filter_feature_from_keep_list.pl --gff infile.gff --keep_list file.txt [ --output outfile ] agat_sp_filter_feature_from_keep_list.pl --help
-f, --reffile, --gff or -ref
Input GFF3 file that will be read
-p, --type 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 into account. fill the option by the value "all" will have the same behaviour.
--kl or --keep_list
Keep list. One value per line.
-a or --attribute
Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID
-o or --output
Output GFF file. If no output file is specified, the output will be written to STDOUT.
Verbose option for debugging purpose.
-h or --help
Display this helpful text.