```sh
agat_convert_genscan2gff.pl --help
```
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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------

Name:
    agat_convert_genscan2gff.pl

Description:
    The script takes a genscan file as input, and will translate it in gff
    format. The genscan format is described here:
    http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
    can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
    sequence, wihtout any header!! Indeed the tool expects only DNA
    sequences and does not crash/warn if an header is submited along the
    sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
    nucleotides of the sequence. Then all prediction location are shifted
    accordingly. (checked only on the online version
    http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
    pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\

Usage:
        agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
        agat_convert_genscan2gff.pl -h

Options:
    --genscan or -g
            Input genscan bed file that will be convert.

    --source
            The source informs about the tool used to produce the data and
            is stored in 2nd field of a gff file. Example:
            Stringtie,Maker,Augustus,etc. [default: data]

    --primary_tag
            The primary_tag corresponf to the data type and is stored in 3rd
            field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]

    --inflate_off
            By default we inflate the block fields (blockCount, blockSizes,
            blockStarts) to create subfeatures of the main feature
            (primary_tag). Type of subfeature created based on the
            inflate_type parameter. If you don't want this inflating
            behaviour you can deactivate it by using the option
            --inflate_off.

    --inflate_type
            Feature type (3rd column in gff) created when inflate parameter
            activated [default: exon].

    --verbose
            add verbosity

    -o , --output , --out , --outfile or --gff
            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.

Feedback:
  Did you find a bug?:
    Do not hesitate to report bugs to help us keep track of the bugs and
    their resolution. Please use the GitHub issue tracking system available
    at this address:

                https://github.com/NBISweden/AGAT/issues

     Ensure that the bug was not already reported by searching under Issues.
     If you're unable to find an (open) issue addressing the problem, open a new one.
     Try as much as possible to include in the issue when relevant:
     - a clear description,
     - as much relevant information as possible,
     - the command used,
     - a data sample,
     - an explanation of the expected behaviour that is not occurring.

  Do you want to contribute?:
    You are very welcome, visit this address for the Contributing
    guidelines:
    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
