agat_sp_filter_feature_by_attribute_value.pl

DESCRIPTION

The script aims to filter features according to attribute value (9th column).

  • If the attribute exists and the value do not pass the test, the feature is written into .

  • If the attribute exists and the value pass the test, the feature is discarded and written into _discarded.gff.

  • If the attribute tag is missing (test cannot be applyed), the feature will be written into by default. If --na_aside parameter is activated then it will be written into _na.gff.

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. /!\ Removing all children of a feature will automatically remove this feature too (excepted if --keep_parental is activated). /!\ If --keep_parental is not activated and --na_aside is activated, and all level3 features of a record are split between both _na.gff and _discarded.gff, then the parental level1 and level2 features are removed and will end up in the _na.gff file only.

SYNOPSIS

agat_sp_filter_feature_by_attribute_value.pl --gff infile.gff --value 1 -t "=" [ --output outfile ]
agat_sp_filter_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(s) to check in the attribute. Case sensitive. List of values must be coma separated.

  • --value_insensitive

    Bolean. Deactivated by default. When activated the values provided by the --value parameter are handled case insensitive.

  • <--na_aside

    Bolean. Deactivated by default. By default if the attribute tag on which the filter is based is missing, the feature will be written into . When activated, such features will be written into a separate file called _na.gff.

  • <--keep_parental>

    Bolean. Deactivated by default. When activated even if all child features have been removed, the parental one will be kept.

  • -t or --test

    Test to apply (> < = ! >= <=). default value "=". If you use one of these two character >, <, please don't forget to quote the parameter like that "<=" otherwise your terminal will complain. Only = and ! tests can be used to compare string values.

  • -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.