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agat_sq_add_hash_tag.pl#

DESCRIPTION#

The script aims to introduce hash tag (####) into the file. It allows for some tools using gff3 to handle independantly file chucks separated by the #### signal. Can make them more efficient.

SYNOPSIS#

agat_sq_add_hash_tag.pl -i <input file> [-o <output file>]
agat_sq_add_hash_tag.pl --help

OPTIONS#

  • --gff, --file or --input

    STRING: Input GTF/GFF file.

  • -i or --interval

    Integer: 1 or 2. 1 will add #### after each new sequence (column1 of the gff), while 2 will add the ### after each group of feature (gene). By default the value is 1.

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • -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).

  • --help or -h

    Display this helpful text.