agat_sp_move_attributes_within_records.pl

DESCRIPTION

The script aims to keep move attributes within a record e.g. from Level1 to Level2 and/or Level3 features; and / or from Level2 to Level2 or Level3 features; and / or from Level3 to Level3 features. Example of L1 feature: gene Example of L2 featrue

SYNOPSIS

agat_sp_move_attributes_within_records.pl --gff infile.gff --feature_copy mRNA  --feature_paste CDS --attribute Dbxref,Ontology [ --output outfile ]
agat_sp_move_attributes_within_records.pl --help

OPTIONS

  • -f, --reffile, --gff or -ref

    Input GFF3 file that will be read

  • --feature_copy or --fc

    primary tag (feature type) option to list from which feature we will copy the attributes, case insensitive. You can specified a feature (or a coma separated list) by giving its primary tag / feature type (column 3) value as: cds, Gene, MrNa, etc You can specify directly all the feature of a particular level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By default all level2 feature are used.

  • --feature_paste or --fp

    primary tag (feature type) option to list to which feature we will paste the attributes, case sensitive. You can specified a feature (or a coma separated list) by giving its primary tag / feature type (column 3) value as: cds, Gene, MrNa, etc 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 level3 are used.

  • -a or --attribute

    Attribute that will be copied and pasted. Case sensitive. You can specified an attribute (or a coma separated list) by giving its attribute tag value (column9) as: Ontology, Dbxref, etc Default: all_attributes /!\ <all_attributes> is a specific parameter meaning all the attributes will be use.

  • -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.