agat_sp_select_feature_by_attribute_value.pl

DESCRIPTION

The script aims to filter features according to attribute value (9th column). If the attribute tag is missing the feature will not be discarded. If the attribute exists and the value pass the test, the feature is discarded. Attribute are stored in the 9th column and have this shape: tag=value /!\ 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_select_feature_by_attribute_value.pl --gff infile.gff --value 1 -t "=" [ --output outfile ]
agat_sp_select_feature_by_attribute_value.pl --help

OPTIONS

  • -f, --reffile, --gff or -ref

    Input GFF3 file that will be read

  • -a or --attribute

    Attribute tag to specify the attribute to analyse (attribute example: tag=value).

  • -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.

  • --value

    Value to check in the attribute

  • -t or --test Test to apply (> < = >= <=). default value "=". If you us one of these two character >, <, please don't forget to quote you parameter liket that "<=". Else your terminal will complain.

  • -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.