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.

• -h or --help

  Display this helpful text.