agat_convert_sp_gff2zff.pl

DESCRIPTION

The script converts GTF/GFF file into zff file a format used by the ab initio tool SNAP. The script produces a .ann file containing the annotation and .dna file containing the fasta file. The .ann and .dna are identicaly sorted by sequence identifier (This is mandatory for usage with fathom).

SYNOPSIS

agat_convert_sp_gff2zff.pl --gff file.gff  --fasta file.fasta [ -o outfile ]
agat_convert_sp_gff2zff.pl --help

OPTIONS

  • --gff

    Input GTF/GFF file

  • --fasta

    Input fasta file

  • --outfile, --out, --output, or -o

    File prefix where will be written the results (e.g. outfile.ann and outfile.dna). 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.