agat_sp_filter_feature_from_kill_list.pl

DESCRIPTION

The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too.

SYNOPSIS

agat_sp_filter_feature_from_kill_list.pl --gff infile.gff --kill_list file.txt  [ --output outfile ]
agat_sp_filter_feature_from_kill_list.pl --help

OPTIONS

• -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 --kill_list

  Kill 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.

• -v

  Verbose option for debugging purpose.

• -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.