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.