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agat_sp_manage_IDs.pl#

DESCRIPTION#

The script takes a gff3 file as input and will go through all feature to overwrite the value of the ID attribute. By default the ID is built as follow: primary_tag(i.e. 3rd column)-Number. If you provide a specific prefix the ID is built as follow: $opt_prefix.$letterCode.Number. By default the numbering start at 1, but you can decide to change this value using the --nb option. The $letterCode is the first letter of the feature type (3rd colum). It is uniq for each feature type, i.e. when two feature types start with the same letter, the second one met will have the two first letter as $letterCode (and so one).

SYNOPSIS#

agat_sp_manage_IDs.pl --gff file.gff -p level2 -p cds -p exon [ -o outfile ]
agat_sp_manage_IDs.pl --help

OPTIONS#

  • --gff or -f

    Input GTF/GFF file.

  • --gap

    Integer - Increment the next gene (level1 feature) suffix with this value. Defauft 0.

  • --ensembl

    Boolean - For an ID Ensembl like (e.g PREFIXG00000000022). The ID is built as follow: $opt_prefix.$letterCode.0*.Number where the number of 0 is adapted in order to have 11 digits.

  • --prefix

    String - Add a specific prefix to the ID. By defaut if will be the feature type (3rd column).

  • --type_dependent

    Boolean - Activate type_dependent numbering. The number is depedendent of the feature type. i.e instead of: NbV1Ch01 AUGUSTUS gene 97932 99714 0.06 - . ID=gene1 NbV1Ch01 AUGUSTUS mRNA 97932 99714 0.06 - . ID=mRNA2 NbV1Ch01 AUGUSTUS exon 97932 98571 . - . ID=exon3 NbV1Ch01 AUGUSTUS exon 98679 98844 . - . ID=exon4 You will get: NbV1Ch01 AUGUSTUS gene 97932 99714 0.06 - . ID=gene1 NbV1Ch01 AUGUSTUS mRNA 97932 99714 0.06 - . ID=mRNA1 NbV1Ch01 AUGUSTUS exon 97932 98571 . - . ID=exon1 NbV1Ch01 AUGUSTUS exon 98679 98844 . - . ID=exon2

  • --collective

    Boolean - In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations like CDS, UTR) we set a uniq ID by default. If you wish to set the a collective ID for those feature, please activate this option.

  • --tair

    Boolean - Tair like Output:

    NbV1Ch01 TAIR10 gene 5928 8737 . - . ID=AT1G01020 NbV1Ch01 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1 NbV1Ch01 TAIR10 exon 5928 8737 . - . ID=AT1G01020.1-exon1

  • --nb

    Integer - Start numbering to this value. Default 1.

  • -p, -t 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 taken into account. fill the option by the value "all" will have the same behaviour.

  • -o , --output , --out or --outfile

    String - 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

    Boolean - Display this helpful text.