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agat_sp_manage_attributes.pl#

DESCRIPTION#

The script removes choosen attributes of selected features. It can also create new attribute with 'empty' value, or copy paste an existing attribute using a new specified tag. Attribute in a gff file have this shape (2 attributes here): tag=value;tag=value and are stored within the 9th column.

SYNOPSIS#

agat_sq_manage_attributes.pl --gff file.gff  --att locus_tag,product,name/NewName -p level2,cds,exon [ -o outfile ]
agat_sq_manage_attributes.pl --help

OPTIONS#

  • --gff or -f

    Input GTF/GFF file.

  • -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 in account.

  • --tag, --att

    Attributes with the tag specified will be removed from the feature type specified by the option p (primary tag). List of tag must be coma separated. /! You must use "" if name contains spaces. Instead to remove an attribute, you can replace its Tag by a new Tag using this formulation tagName/newTagName. To remove all attributes non mandatory (only ID and Parent are mandatory) you can use the option with <all_attributes> parameter.

  • --add

    Attribute with the tag specified will be added if doesn't exist. The value will be 'empty'.

  • --cp

    When tags specied are with this form: tagName/newTagName. By using this <cp> parameter, the attribute with the tag tagName will be duplicated with the new tag newTagName if no attribute with the tag newTagName already exits.

  • --overwrite

    When using --add parameter, if an attribute with the specificed tag already exists, it will not be modified. When using --cp parameter, if an attribute with the specificed newTagName already exists, it will not be modified. So using the --overwrite parameter allows to overwrite the value of the existing attribute.

  • --value

    String. When a value is provided the attribute is taken into account only if the attribute contains (or match) a specific value

  • --strategy

    String. [Default equal]. Strategy to use when --value parameter is in use. Can be equal or match. Equal => the attribute value must be identical. Match => the attribute value must match

  • -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.